\n \n
\n \n\nCustomers with PathcoreFlow deployed to an on-premise server or virtual machine (VM) will receive an email notification from Pathcore Support when a new version of the software is available.\n\n
\n It is recommended to perform a backup before making any changes.\n
\n\n
\n It is recommended to keep the operating system of the server or VM hosting PathcoreFlow up to date. Instructions for maintaining your OS should be available from the vendor.\n
\n\n\n\n
\n It is recommended to keep Docker Engine updated to the latest stable version. If you are running on one of their supported platforms, then these updates may be available in the same manner as other software updates.\n
\n It is recommended that you review the update process as well as any additional files and instructions provided with the announcement before proceeding.\n
\n\n\n\n
\n These steps assume you have installed PathcoreFlow in the default directory:
/opt/pathcore.\n\n\n \n\n 4. You may be asked to provide the UID (User ID) and GID (Group ID) of the user that should own the database files. The suggested value should work for most deployments, but check with your system administrator if unsure\n\n 5. The installer script will do some initial checks, and display a summary of the changes to be performed. You will be prompted to confirm before any changes are made\n\n 6. You will be given the option to (re)install the systemd service. This is recommended if your operating system uses the [systemd](https://systemd.io/) service manager\n\n 7. A summary is displayed after updating, and your PathcoreFlow service should be available with the new version\n\n\n \n\n
\n\nTo update PathcoreFlow
\n\n\n This will cause the PathcoreFlow services to be temporarily unavailable.\n
\n\n 1. Ensure you have a recent backup.\n\n 2. Transfer the installer script to the server or VM hosting PathcoreFlow. This is typically done via [SSH File Transfer Protocol (SFTP)](https://en.wikipedia.org/wiki/SSH_File_Transfer_Protocol) (e.g., the `scp` command) to somewhere temporary (e.g., `/tmp`)\n\n 3. Log in to the server or VM hosting PathcoreFlow and run the installer script, e.g.:\n\n ```bash\n bash /tmp/pathcoreflow-v4.2.0-installer.sh\n ```\n\n \n The script should be executed by a user with
sudo access. Your password may be requested to perform some tasks.\n \n If you encounter a problem when updating, please contact Pathcore Support for assistance.\n
\n\n
\n\n\n\n When using the installer script to perform an update, another script to rollback to the previously installed version will be placed in the `compose/scripts/` directory. This script will be named `pathcoreflow-vX.Y.Z-rollback.sh`, where \"vX.Y.Z\" is the previously installed version. For example, after updating from PathcoreFlow v4.1.3 to v4.2, the file would be `pathcoreflow-v4.1.3-rollback.sh`.\n\n
\n\n\n## Support\n\nPathcore also offers specialized technical support services designed for on-premise deployments. These services are designed to support customer IT teams with installation and maintenance of Pathcore software.\n\nThese services can accommodate non-standard deployments and provide custom solutions when required. Ask your account manager for more information about support services we offer.\n","slug":"docs/on-premise/update"},{"frontmatter":{"title":"Requirements","description":"requirements"},"rawBody":"---\ntitle: Requirements\ndescription: requirements\norder: 20\nsection: PathcoreFlow\n---\n\n\n# Requirements\n\nTo rollback an update to PathcoreFlow
\n\n\n This action is potentially dangerous. Please ensure you have a recent backup before proceeding.\n
\n\n \n\n
\n If you encounter a problem when updating or believe there is a need to revert to an earlier version of PathcoreFlow, it is recommended that you contact Pathcore Support for assistance.\n
\n\n## Client Requirements\n\nPathcoreFlow is an entirely browser-based application. No additional software needs to be installed on client machines.\n\n### Web Browser Requirements\n\nPathcoreFlow is officially supported in the following web browsers:\n\n- Google Chrome (last 2 versions)\n- Mozilla Firefox (last 2 versions)\n- Apple Safari (last 2 versions)\n- Microsoft Edge (last 2 versions)\n\nIt is likely that the PathcoreFlow application will be functional in older versions of the listed browsers, with the exception of Internet Explorer. The software may also function in browsers not listed here.\n\n## System Requirements\n\nPathcore recommends that client machines meet the following minimum system requirements:\n\n- Dual core CPU at 2 Ghz\n- 8 GB RAM\n- 100 Mbps network interface\n\n\n## Server Requirements\n\nFor information about the requirements for hosting your own PathcoreFlow server, see the [Technical Requirements](/docs/on-premise/technical-requirements/) page in the [On-Premise](/docs/on-premise/) section.\n","slug":"docs/overview/requirements"},{"frontmatter":{"title":"Supported Formats","description":"supported formats"},"rawBody":"---\ntitle: Supported Formats\ndescription: supported formats\norder: 30\nsection: PathcoreFlow\n---\n\n# Supported Formats\n\n
\n\n## Attachments\n\nAny data file can be uploaded into the Repository. Where possible, the files are automatically identified and labeled as an \"Attachment\" if their contents are not viewable in the Viewer. Some attachments, such as PDF files and MS Office files may be viewable in your browser or with an application you have on your computer. In all other cases, attachments can be downloaded and processed with the appropriate application.\n\n## Supported Image Formats\n\nThe Viewer supports many proprietary whole slide image formats, DICOM standard whole slide images, some DICOM radiology formats as well common image formats.\n\n| Vendor | Format |\n| ----------- | ---------- |\n| 3DHISTECH | MRXS |\n| Aperio | SVS |\n| Aperio | AFI |\n| Hamamatsu | VMS |\n| Hamamatsu | VMU |\n| Hamamatsu | NDPI |\n| Hamamatsu | NDPIS |\n| Leica | SCN |\n| Lunaphore | OME-TIFF |\n| Motic | Motic SVS |\n| Olympus | VSI |\n| OME | OME-TIFF |\n| PerkinElmer | QPTIFF |\n| Sakura | SVSlide |\n| Ventana | BIF |\n| Ventana | TIF |\n| Zeiss | CZI |\n| | Tiled TIFF |\n| | BigTIFF |\n| | JPEG2000 |\n| | DICOM |\n| | BMP |\n| | JFIF |\n| | PNG |\n\n### Known Limitations\n\nThe following image types are known to not work with PathcoreFlow:\n- Images without a pyramid (e.g., TIFF or PNG) are much slower to render as they grow in size, which can lead to timeouts\n- VSI images with a grid offset are not supported\n- MRXS images without an `.mrxs` file are not supported\n - The scanner may not produce this file, but CaseViewer will create it if it does not already exist when it opens the image for viewing\n- OME-TIFF images which contain JPEG2000 compressed data are not supported\n - VSI images which are exported to OME-TIFF may contain JPEG2000 compressed data\n- Multi-file DICOM images are not supported\n- Multi-file OME-TIFF images are not supported\n\nCertain operations are guarded with a restriction on the maximum area that can be processed (42,000,000 pixels by default). The following requests can fail for images exceeding that limit:\n- Region requests\n- Thumbnail requests\n- Nikon tile requests\n\nThe following actions are not performed by PathcoreFlow's image processing:\n- Reading embedded metadata not directly related to the image data (e.g., patient, study)\n- Reading embedded annotations out of formats such as MRXS and VSI\n- Handling of files which have been modified after they appear in the Repository (when using the image indexing service)\n","slug":"docs/overview/supported-formats"},{"frontmatter":{"title":"Detailed Template Example","description":"detailed template example"},"rawBody":"---\ntitle: Detailed Template Example\ndescription: detailed template example\nsection: Report Templates\norder: 37\n---\n\n# Detailed Template Example\n\n
\n\nThe following is a larger report template example that illustrates various features including:\n\n| Feature Example | Syntax |\n| ------------------------------------------------- | ----------------------------------------------------------- |\n| Displaying variables | `{{ folder.name }}` |\n| Using filters |
{{ at.filesize \\| filesizeformat }} |\n| Looping over lists of data | `{% for im in folder.images %}` |\n| Checking conditions | `{% if report_signed_by %}` |\n| Accessing static data | `{% for item in static_data['foo'] %}` |\n| Accessing the list of images in the folder | `{% for im in folder.images %}` |\n| Accessing the list of snapshots for a given image | `{% for snapshot in im.snapshots %}` |\n| Accessing snapshots in a container | `{% for snapshot in snapshots['container1'] %}` |\n| Displaying image thumbnails | `\n {#\n Add any text such as a report title or description of the report anywhere in the\n report template using different HTML blocks such as paragraph tags /
![](\"{{)
\n {# Displays a portion of the full size image #}\n \n {# Displays the slide label of the image (if available) #}\n \n
\n{% endblock %}\n```\n","slug":"docs/report-templates/detailed-template-example"},{"frontmatter":{"title":"Overview","description":"overview"},"rawBody":"---\ntitle: Overview\ndescription: overview\norder: 10\nsection: PathcoreFlow\n---\n\n\n# PathcoreFlow\n\n,\n line breaks
, headings
/ / etc.\n #}\n\n Detailed Report
\n\n
Detailed Report
\n\n\n Use variables passed to the template like this: The name of the case is {{ case.name }}.\n
\n\nFolder Name
\n {# Displays the currently selected folder's name #}\n {{ folder.name }}\n\nFolder ID
\n {# Displays the currently selected folder's ID in PathcoreFlow #}\n {{ folder.id }}\n\nFolder Description
\n {# Displays the currently selected folder's description #}\n {{ folder.description }}\n\nCustom Fields
\n {# Displays all the Custom Fields associated with the folder #}\n {{ folder.fields }}\n\nStatic Data
\n- \n {# Begins looping through the static data array called 'foo' #}\n {% for item in static_data['foo'] %}\n {# Outputs each item in the 'foo' array #}\n
- {{ item }} \n {% endfor %}\n
\n Name: {{ static_data['name'] }}
\n Date: {{ static_data['date'] }}\n
Images
\n {# Begins looping through all the images in the currently selected folder #}\n {% for im in folder.images %}\n {# Outputs the properties of each image #}\n {# Outputs the image name, ID, filesize #}\n{{ im.name|e }} (ID: {{ im.id }}) ({{ im.filesize | filesizeformat }})
\n {# Displays the actual image as a thumbnail #}\nSnapshots
\n {# Snapshots and snapshot metadata for each image can also be displayed #}\n {% for snapshot in im.snapshots %}\n {# Displays the title, id and description of each snapshot #}\n\n \n
\n {% else %}\n Title: {{ snapshot.title }}
\nID: {{ snapshot.id }}
\nDescription: {{ snapshot.description }}
\n {# Displays the snapshot #}\nNo snapshots!
\n {% endfor %}\n {% endfor %}\n\nAttachments
\n- \n {# Begins looping through all the attachments in the currently selected folder #}\n {% for at in folder.attachments %}\n
- \n {# Outputs the attachment name and filesize #}\n {{ at.name }} ({{ at.filesize | filesizeformat }})\n {# Outputs the attachment URL #}\n {{ at.file_url }} \n \n {% endfor %}\n
Snapshots
\n {# Snapshots can also be displayed without accessing their associated image #}\n {# Begins looping through all the snapshots in the snapshot container 'container1' #}\n {% for snapshot in snapshots['container1'] %}\n {# Displays the title, id and description of each snapshot #}\n\n \n
\n {% endfor %}\n\n Title: {{ snapshot.title }}
\nID: {{ snapshot.id }}
\nDescription: {{ snapshot.description }}
\n {# Displays the snapshot #}\nIf the report is signed, the signer's signature and name will appear here:
\n {% if report_signed_by %}\n\n \n
\n {% endif %}\nSigned by {{ report_signed_by.name }} at {{ report_signed_at }}
\n\n\nPathcoreFlow is an enterprise workspace for digital pathology, with a focus on whole slide image management.\nIt consists of several tools for organization and collaboration, including the [Repository](/docs/repository/repository-overview/) — a virtual file system that is accessible from any internet-enabled device — and the [Viewer](/docs/viewer/overview/) — an image viewer optimized for whole slide images and that supports a [range of formats](/docs/overview/supported-formats/) from many scanner vendors.\n","slug":"docs/overview/"},{"frontmatter":{"title":"","description":null},"rawBody":"---\nredirect: /docs/report-templates/report-templates-overview/\n---\n","slug":"docs/report-templates/"},{"frontmatter":{"title":"Auxiliary Information","description":"auxiliary information"},"rawBody":"---\ntitle: Auxiliary Information\ndescription: auxiliary information\nsection: Report Templates\norder: 36\n---\n\n\n# Auxiliary Information\n\n
\n\n\n## Styles\n\nReport templates in PathcoreFlow use Cascading Style Sheets (CSS) to style the generated reports. More information about the supported CSS specifications can be found in the [WeasyPrint documentation](https://doc.courtbouillon.org/weasyprint/stable/api_reference.html#css)\n\n### Style Example\n\nThis example CSS style will set the font to sans-serif for the container class, sets the max width to 3 inches and text aligned to center for the signature class, sets the max width of an image in the signature class to 100%, and creates a border around any images.\n\n```css\n/* Define your CSS styles here */\n\n.container {\n font-family: sans-serif;\n}\n\n.signature {\n max-width: 3in;\n text-align: center;\n}\n\n.signature img {\n max-width: 100%;\n}\n\nimg {\n border-style: solid;\n}\n```\n\n\n## Static Data\n\nPredefined data can be added to a report in a flexible way by adding it to the **Static Data** tab. Data entered there can be accessed inside the template via the variable `static_data`. The data is specified using the JavaScript Object Notation (JSON) format. See this [introduction to JSON syntax](https://www.w3schools.com/js/js_json_syntax.asp) for more information.\n\n### Static Data Example\n\nThis section shows the report template code to display output from `static_data`.\n\n```\n
Static Data
\n\n- \n{# Begins looping through the static data array called 'foo' #}\n{% for item in static_data['foo'] %}\n {# Outputs each item in the 'foo' array #}\n
- {{ item }} \n{% endfor %}\n
\n Name: {{ static_data['name'] }}
\n Date: {{ static_data['date'] }}\n
\n\n
\n\nTo create a snapshot container
\n\n 1. Open a report template for editing. See [Working With Reports](/docs/report-templates/working-with-reports/) for details\n\n 2. Click on the **Snapshots** tab\n\n 3. Click on the **+ Add Snapshot Container** button\n\n 4. Type a name for the container in the **Display Name** field\n\n 5. Type a value in the **Template Name** field\n - This is the name of the snapshot container used within the report template. For example, if you name the container \"selected\\_features\", the list of snapshots would be accessed as the variable `snapshots.selected_features`\n\n 6. (Optional) Enable the **Required** toggle if the report must contain snapshots\n\n 7. Set the **between** values to the range of snapshots allowed or required in the report. (i.e., to force the user to select up to 5 snapshots to be included in the report, set **between** values to 1 and 5)\n\n\n\n
\n\n### Snapshots Example\n\n```\n{# Begins looping through all the snapshots in the snapshot container 'container1' #}\n{% for snapshot in snapshots['container1'] %}\n {# Displays the title, id and description of each snapshot #}\n To delete a snapshot container
\n\n 1. Open a report template for editing. See [Working With Reports](/docs/report-templates/working-with-reports/) for details\n\n 2. Click on the **Snapshots** tab\n\n 3. Locate the container to be removed\n\n 4. Click on the  button at the bottom left of the container block\n\n\n \n
\n{% endfor %}\n```\n","slug":"docs/report-templates/auxiliary-information"},{"frontmatter":{"title":"Jinja2 Quick Reference","description":"jinja2 quick reference"},"rawBody":"---\ntitle: Jinja2 Quick Reference\ndescription: jinja2 quick reference\nsection: Report Templates\norder: 34\n---\n\n\n# Jinja2 Quick Reference\n\nTitle: {{ snapshot.title }}
\nID: {{ snapshot.id }}
\nDescription: {{ snapshot.description }}
\n {# Displays the snapshot #}\n\n\nThis section provides an overview of the syntax and some of the commonly used features of the Jinja2 templating language. For more detailed information, refer to the official [Jinja2 documentation](https://jinja.palletsprojects.com/en/3.0.x/templates/).\n\n
\n As the template engine is very flexible, the configuration from the PathcoreFlow application can be slightly different from the code presented here in terms of delimiters and behavior of undefined values. If you encounter any anomalies, contact our support team.\n
\n\n\n## Basic Syntax\n\nA template contains variables and/or expressions, which get replaced with values when a template is rendered; and tags, which control the logic of the template.\n\nThere are a few kinds of delimiters configured as follows:\n\n```\n{% ... %} for Statements\n{{ ... }} for Expressions to print to the template output\n{# ... #} for Comments not included in the template output\n```\n\n\n## Variables\n\nVariables may have attributes or elements on them you can access. See the [Placeholder Reference](/docs/report-templates/placeholder-reference/) for details.\n\nYou can use a dot (`.`) to access attributes of a variable in addition to the standard subscript (`[]`) syntax.\n\nThe following lines do the same thing:\n\n```\n{{ folder.image }}\n{{ folder['image'] }}\n```\n\nIt’s important to know that the outer two curly braces are not part of the variable, but the print statement. If you access variables inside tags, don't put the braces around them. If a variable or attribute does not exist, you will get back an undefined value.\n\n\n## Filters\n\nVariables can be modified by filters. Filters are separated from the variable by a pipe symbol (`|`) and may have optional arguments in parentheses. Multiple filters can be chained. The output of one filter is applied to the next.\n\nFor example, `{{ name|striptags|title }}` will remove all HTML Tags from variable \"name\" and title-case the output (i.e., `title(striptags(name))`).\n\nFilters that accept arguments have parentheses around the arguments, just like a function call. For example: `{{ listx|join(', ') }}` will join a list with commas (i.e., `str.join(', ', listx)`).\n\nThe [List of Builtin Filters](https://jinja.palletsprojects.com/en/3.0.x/templates/#list-of-builtin-filters) in the official Jinja2 documentation describes all the builtin filters.\n\n\n## Tests\n\nBeside filters, there are also so-called \"tests\" available. Tests can be used to test a variable against a common expression. To test a variable or expression, you add `is` plus the name of the test after the variable. For example, to find out if a variable is defined, you can do `name is defined`, which will then return true or false depending on whether name is defined in the current template context.\n\nTests can accept arguments, too. If the test only takes one argument, you can leave out the parentheses. For example, the following two expressions do the same thing:\n\n```\n{% if loop.index is divisibleby 3 %}\n{% if loop.index is divisibleby(3) %}\n```\n\nThe [List of Builtin Tests](https://jinja.palletsprojects.com/en/3.0.x/templates/#builtin-tests) in the official Jinja2 documentation describes all the builtin tests.\n\n\n## Comments\n\nTo comment out part of a line in a template, use the comment syntax which is `{# ... #}`. This is useful to comment out parts of the template for debugging or to add information for other template designers or yourself:\n\n```\n{# note: commented-out template because we no longer use this\n {% for user in users %}\n ...\n {% endfor %}\n#}\n```\n\n\n## Control Structures\n\nA control structure refers to all those things that control the flow of a program - conditionals (i.e., if/elif/else), for-loops, as well as things like macros and blocks. Control structures appear inside `{% ... %}` blocks.\n\n### For\n\nLoop over each item in a sequence. For example, to display a list of image names provided in the selected folder:\n\n```\nImages
\n- \n{% for im in folder.images %}\n
- {{ im.name|e }} \n{% endfor %}\n
- \n{% for key, value in folder.fields.items() %}\n
- {{ key|e }} \n
- {{ value|e }} \n{% endfor %}\n
\n The \"e\" in the above examples is an alias for the builtin escape filter. The escape filter converts the characters &, <, >, ', and \" in a string to HTML-safe sequences. Use this if you need to display text that might contain such characters.\n
\n\nNote, however, that dicts are not ordered; so you might want to use the `dictsort` filter.\n\nInside of a for-loop block, you can access some special variables:\n\n| Variable | Description |\n| ---------------- | ------------------------------------------------------------------------------------ |\n| `loop.index` | The current iteration of the loop. (1 indexed). |\n| `loop.index0` | The current iteration of the loop. (0 indexed). |\n| `loop.revindex` | The number of iterations from the end of the loop (1 indexed). |\n| `loop.revindex0` | The number of iterations from the end of the loop (0 indexed). |\n| `loop.first` | True if first iteration. |\n| `loop.last` | True if last iteration. |\n| `loop.length` | The number of items in the sequence. |\n| `loop.cycle` | A helper function to cycle between a list of sequences. See the explanation below. |\n| `loop.depth` | Indicates how deep in a recursive loop the rendering currently is. Starts at level 1. |\n| `loop.depth0` | Indicates how deep in a recursive loop the rendering currently is. Starts at level 0. |\n\nUnlike in Python, it’s not possible to break or continue in a loop. You can, however, filter the sequence during iteration, which allows you to skip items. The following example skips images with the name \"test\":\n\n```\n{% for im in folder.images if not im.name == 'test' %}\n - \n{% for im in folder.images %}\n
- {{ im.name }} \n{% else %}\n
- No image found \n{% endfor %}\n
\n \n
\n\n{% endif %}\n```\n","slug":"docs/report-templates/jinja2-quick-reference"},{"frontmatter":{"title":"Report Templates Overview","description":"working with figures"},"rawBody":"---\ntitle: Report Templates Overview\ndescription: working with figures\nsection: Report Templates\norder: 32\n---\n\n\n# Report Templates Overview\n##### [add-on]\n\nReport templates may be used to generate standardized PDF outputs for summarizing the information in a folder. Reports may include the signature of the user that generated them and are automatically saved in the folder where they are generated. Report templates provide a convenient mechanism for archiving and/or sharing study information in standard formats. Different report templates can be used for different studies, depending on the need.\n\nSigned by {{ report_signed_by.name }} at {{ report_signed_at }}
\n\n The Report templates add-on is required to create reports.\n
\n\n\n## Developing Templates\n\nDeveloping templates requires understanding of HTML and CSS. If you don’t have the required expertise and are not willing to experiment, contact our support team for information on how we may be able to support you.\n\nThe style and layout of the data in a template can be fully customized with standard HTML and CSS, similar to how web pages are formatted. Additionally, placeholders can be used to represent metadata, snapshots, image thumbnails, hyperlinks, as well as other static data (e.g., text and images) throughout the template. During report generation, these placeholders are populated with data from the folder in which the report is generated. The output of the reporting engine is a PDF that has been formatted and populated according to the template that has been used.\n\nTo better understand the features of the templating language, start by reviewing our [Jinja2 Quick Reference](/docs/report-templates/jinja2-quick-reference/) and [Placeholder Reference](/docs/report-templates/placeholder-reference/). For comprehensive information about the templating language, refer to the [Jinja2 documentation](https://jinja.palletsprojects.com/en/3.0.x/templates/).\n\n\n### A Basic Template\n\nThe following example demonstrates a trivial example of a template that outputs the list of images in a folder. To learn more about the syntax and possibilities, see the following pages for more details: [Jinja2 Quick Reference](/docs/report-templates/jinja2-quick-reference/), [Placeholder Reference](/docs/report-templates/placeholder-reference/) and [Auxiliary Information](/docs/report-templates/auxiliary-information/).\n\n```\n{# Section for report title #}\n{% block title %}\n {# Set the title of your PDF document in this block (text only) #}\n{% endblock %}\n\n{# Section for report body #}\n{% block body %}\n\n
\n{% endblock %}\n```\n","slug":"docs/report-templates/report-templates-overview"},{"frontmatter":{"title":"Placeholder Reference","description":"placeholder reference"},"rawBody":"---\ntitle: Placeholder Reference\ndescription: placeholder reference\nsection: Report Templates\norder: 35\n---\n\n\n# Placeholder Reference\n\nBasic Report Template
\n\nSet the content of your report within the \"body\" block.
\nUse variables passed to the template like this:
\nThe name of the folder is {{ folder.name }}.
\n\nList of Images
\n- \n {% for im in folder.images %}\n
- \n {{ im.name }} ({{ im.filesize | filesizeformat }})\n \n {% endfor %}\n
If the report is signed, the signer's signature and name will appear here:
\n {% if report_signed_by %}\n\n \n
\n {% endif %}\nSigned by {{ report_signed_by.name }} at {{ report_signed_at }}
\n\n\nThere are a number of placeholders that can be used within report templates. These include global variables and functions, and various data types.\n\n\n## Global Variables\n\n| Name | Type | Description |\n| ------------------ | ------------------------ | ------------ |\n| `static_data` | dict | Contains the static data specified in the Static Data tab of the report template editor. |\n| `folder` | Folder | Contains data related to the folder this report is being rendered for. |\n| `case` | Folder | Alias of folder. |\n| `snapshots` | dict{string: Snapshot[]} | Snapshots selected by the report generator, grouped by snapshot container. Keys in the dict are the template names specified in the snapshot containers section of the report template editor. |\n| `report_signed_by` | Signer | The signer of the report (if it is signed). |\n| `report_signed_at` | datetime | When the report was signed (if it was signed). |\n\n\n## Global Functions\n\n| Name | Description |\n| ----------------------------- | -------------------------------------------------------------------------------- |\n| `template_file_by_name(name)` | Get a URL to the file contents of a [Report Template File](/docs/report-templates/working-with-reports/#report-template-files) by specifying its name. |\n| `template_file_by_id(id)` | Get a URL to the file contents of a [Report Template File](/docs/report-templates/working-with-reports/#report-template-files) by specifying its id. |\n\n#### Parameters\n\n| Name | Type | Description |\n| ---------- | -------- | --------------------------------------------------------------- |\n| `name` | string | The name of the report template file (must be exact). |\n| `id` | string | The id (10 character alphanumeric) of the report template file. |\n\n\n## Data Types\n\nSome commonly used properties for folders, images, attachments and snapshots are listed.\n\n
\n Some properties are omitted for brevity. The pprint filter in Jinja is useful for exploring the available properties in each variable.\n
\n\n\n## Generating Reports\n\nUsers can generate a report from within a folder. The generated PDF outputs are always saved in the folder where the report is generated.\n\n
\n To be able to generate reports, users require the \"Folders->View\" and \"Files->Upload\" permission flags and need to be able to navigate to a folder and change its contents. In addition, the \"Files->View\" permission flag is required to view a generated report, and the \"Images->View\" permission flag is required to view images that may be linked into a report.\n
\n\n\n\n
\n\n\n## Managing Report Templates\n\nTo better understand the features of the templating language, start by reviewing our [Jinja2 Quick Reference](/docs/report-templates/jinja2-quick-reference/) and [Placeholder Reference](/docs/report-templates/placeholder-reference/). For comprehensive information about the templating language, refer to the [Jinja2 documentation](https://jinja.palletsprojects.com/en/3.0.x/templates/).\n\nTo generate a report from an existing template
\n\n 1. Navigate to any folder in the Repository (click on the  **Repository** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu) then navigate to a folder)\n\n 2. Click on the  button at the top right of the item list\n\n 3. In the popup menu, click **Generate Report**\n\n 4. Type a name in the **Report Name** field\n\n 5. Select a template from the **Report Template** dropdown menu\n\n 6. (Optional) Enable the **Sign report** toggle to insert your signature into the report. To create or update a signature, see [My Account](/docs/settings/my-account/)\n\n 7. (Optional) Click on the **Preview** button to see how the report will render for this folder\n\n 8. Click on the **Generate Report** button. The report will be saved as a PDF into the current folder\n\n\n\n If you don't have this option, it may not be enabled for your team.\n
\n\n\n The Report templates add-on and \"Manage report templates\" permission flag is required to create or edit report templates.\n
\n\n\n\n
\n\nTo create a report template
\n\n 1. Click on the  **Settings** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu)\n\n 2. Click on the **Report Templates** tab\n\n 3. Click on the **New Report Template** button\n\n 4. Type a name for the template into the field at the top of the page\n\n 5. Click on the **Template** tab\n\n 6. Make the desired changes to the template. See [Jinja2 Quick Reference](/docs/report-templates/jinja2-quick-reference/) and [Placeholder Reference](/docs/report-templates/placeholder-reference/) for details\n\n 7. (Optional) Click on the **Styles**, **Static Data**, or **Snapshots** tabs and make desired adjustments. See [Auxiliary Information](/docs/report-templates/auxiliary-information/) for details\n\n 8. (Optional) Preview the template:\n 1. Click on the **Select Folder** button and select a folder for testing\n 2. (Optional) Enable the **Signed** toggle to insert your signature into the report\n 3. Click on the **Generate Preview** button\n\n 9. Click on the **Save** button\n\n\n\n
\n\nTo edit a report template
\n\n 1. Click on the  **Settings** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu)\n\n 2. Click on the **Report Templates** tab\n\n 3. Select a report template from the table\n\n 4. Click on the **Edit** button above the table\n\n 5. (Optional) Edit the name of the template in the field at the top of the page\n\n 6. Click on the **Template** tab\n\n 7. (Optional) Make the desired changes to the template. See [Jinja2 Quick Reference](/docs/report-templates/jinja2-quick-reference/) and [Placeholder Reference](/docs/report-templates/placeholder-reference/) for details\n\n 8. (Optional) Click on the **Styles**, **Static Data**, or **Snapshots** tabs and make desired adjustments. See [Auxiliary Information](/docs/report-templates/auxiliary-information/) for details\n\n 9. (Optional) Preview the template:\n 1. Click on the **Select Folder** button and select a folder for testing\n 2. (Optional) Enable the **Signed** toggle to insert your signature into the report\n 3. Click on the **Generate Preview** button\n\n 10. Click on the **Save** button\n\n\n\n
\n\nTo preview a report template
\n\n 1. Click on the  **Settings** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu)\n\n 2. Click on the **Report Templates** tab\n\n 3. Select a report template from the table\n\n 4. Click on the **Edit** button above the table\n\n 5. Click on the **Select Folder** button and select a folder for testing\n\n 6. (Optional) Enable the **Signed** toggle to insert your signature into the report\n\n 7. Click on the **Generate Preview** button\n\n\n\n
\n\nTo enable or disable a report template
\n\n 1. Click on the  **Settings** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu)\n\n 2. Click on the **Report Templates** tab\n\n 3. Set the **Active** toggle next to the report template's name\n\n\n\n
\n\n\n## Report Template Files\n\nReport template files are static files that are referenced in your report templates (e.g., a logo image). These files can be referenced by name or ID in your template. See [Placeholder Reference - Global Functions](/docs/report-templates/placeholder-reference/#global-functions) for details.\n\nTo delete a report template
\n\n 1. Click on the  **Settings** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu)\n\n 2. Click on the **Report Templates** tab\n\n 3. Select a report template from the table\n\n 4. Click on the **Delete** button above the table\n\n 5. Click on the **Yes** button to confirm\n\n\n\n
\n\nTo upload a report template file
\n\n 1. Click on the  **Settings** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu)\n\n 2. Click on the **Report Templates** tab\n\n 3. Click on the **Upload** button in the **Report Template Files** section of the page\n\n 4. Click in the blue box to activate the file selection dialog or simply drag files into the blue box; repeat as required for other files\n\n 5. Click on the **Start Upload** button to start upload\n\n 6. Click on the **X** button to minimize the File Uploads dialog\n\n 7. To check upload status, click on the **Details** button from the upload progress notification at the top of the screen\n\n\n\n
\n\nTo rename a report template file
\n\n 1. Click on the  **Settings** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu)\n\n 2. Click on the **Report Templates** tab\n\n 3. Select an item from the table in the **Report Template Files** section of the page\n\n 4. Click on the **Rename** button above the table\n\n 5. In the popup dialog, type a new name for the file\n\n 6. Click on the **Rename** button or press the **Enter** key to save. To discard your changes, click on the **Cancel** button or press the **Escape** key\n\n\n\n
\n","slug":"docs/report-templates/working-with-reports"},{"frontmatter":{"title":"Activity Logs","description":"activity logs"},"rawBody":"---\ntitle: Activity Logs\ndescription: activity logs\norder: 10\nsection: Repository\n---\n\n# Activity Logs\n\nTo delete a report template file
\n\n 1. Click on the  **Settings** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu)\n\n 2. Click on the **Report Templates** tab\n\n 3. Select an item from the table in the **Report Template Files** section of the page\n\n 4. Click on the **Delete** button above the table\n\n 5. Click on the **Yes** button to confirm\n\n\n\nChanges made in the Repository and Viewer are tracked in Activity Logs. The activity log displays a list of all items that have been created, modified, or deleted, as well as information about when and by whom the changes were made. Users can review past actions in the [Activities Tab](#activities-tab) of the right-hand panel in the Repository, and users with the necessary permissions can export the detailed activity logs as a CSV file.\n\n\n## Activities Tab\n##### \\[BioPharma] [Research+]\n\nFrom the Repository, it is possible to review the activity log for an item in the right-hand panel. You can search the list to highlight specific actions, item types, or users.\n\n
\n The \"Preview activities\" permission flag is required to access the Activities tab.\n
\n\n
\n\nTo view the activity log for an item from the Repository
\n\n 1. Navigate to any folder in the Repository (click on the  **Repository** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu) then navigate to a folder)\n\n 2. Select a single item in a folder\n\n 3. Click on the **Activities** tab of the right-hand panel. You may need to click on the  button if the panel is collapsed\n\n 4. (Optional) Type an action, item type, or user name into the search box to highlight matching activities in the list\n\n 5. (Optional) Click on the  button at the top right of the activity list to apply additional display options\n 1. (Optional) Click on **Expand all Details** to show additional details for all entries, or click on **Collapse All Details** to hide them\n 2. (Optional) Enable the **Show Reason for Change (RFC)** toggle to show the user-provided reason for changes in the activity logs. See [Reason for Change Tracking](/docs/settings/policies/#reason-for-change-tracking) for more details\n\n\n\n
\n\n\n## Exporting Activity Logs\n##### [add-on]\n\nIt is possible to export detailed activity logs for an item in the Repository as a CSV file.\n\nTo see additional details for an activity in the log
\n\n 1. In the **Activities** tab, locate the entry for which you want more information\n\n 2. To show or hide the details of an activity, click on its entry in the list\n\n 3. To get the precise date and time of an activity, hover over the relative time (e.g., \"5 days ago\", \"a month ago\") to display the exact time the activity occurred in the local timezone\n\n\n The Exportable activity logs add-on and \"Export activities\" permission flag is required to export activity logs.\n
\n\n\n\n
\n\nTo export activity logs for an item from the Repository
\n\n 1. Navigate to any folder in the Repository (click on the  **Repository** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu) then navigate to a folder)\n\n 2. Bring up the [context menu](/docs/repository/repository-operations/#context-menu) for the item\n\n 3. Click **Export Activities**\n\n 4. (Optional) In the popup dialog, select the start date from the **Since** field\n\n 5. (Optional) Select the desired output timezone from the **Timezone** dropdown menu\n\n 6. Click on the **Export CSV** button to download a CSV file. See [Activity Log File Format](#activity-log-export-format) for more details\n\n\n\n
\n\n\n### Activity Log Export Format\n\nThe exported activity logs are provided in the CSV (comma separated value) file format which is compatible with all popular spreadsheet applications.\n\nBy default, entries are sorted by \"Activity ID\" in ascending order. Each entry in the log file has the following columns:\n\n- **Activity Id**: numeric ID for the action or activity that occurred\n- **Object Id**: numeric ID for the object that was affected\n- **Transaction Time (timezone)**: provides the time of the event in the timezone selected when exporting the logs to CSV\n- **Remote Address**: address of the client which caused the event, if applicable\n- **User ID**: numeric ID of the user which caused the event, if applicable\n- **User Name**: the display name of the user account\n- **User Email**: the email address of the user account\n- **Parent Name**: name of the object's parent\n- **Object Name**: name of the object that was affected\n- **Object Type**: type of the object that was affected\n- **Property**: name of the property of the object that was changed\n- **New Value**: new value of the property that was changed\n- **Old Value**: old value of the property that was changed\n- **Operation**: type of operation performed on the object\n- **Reason for Change**: reason given by the user for the change\n\n#### Object Types\n\n- **attachment**\n- **figure**\n- **folder**\n- **image**\n- **image_overlay**\n- **report**\n\n#### Operations\n\n- **CREATE**: the object was added\n- **PATCH**: the object was changed\n- **DELETE**: the object was removed\n\n\n### Example of an Exported Activity Log\n\nAn example of a CSV file of exported activity logs is available to download below.\n\nThe following actions were performed:\n\n- Create a new folder named \"Example Folder\"\n- Upload the file \"slide_001A.zip\" which is an archive containing the image \"slide_name001A.mrxs\"\n- Add an annotation to the image\n- Rename the annotation to \"Annotation 1\"\n- Delete the image\n\nDownload: activity-logs-example.csv\n","slug":"docs/repository/activity-logs"},{"frontmatter":{"title":"","description":null},"rawBody":"---\nredirect: ../activity-logs/\n---\n","slug":"docs/repository/audit-logs"},{"frontmatter":{"title":"Data Ingestion","description":"data ingestion"},"rawBody":"---\ntitle: Data Ingestion\ndescription: data ingestion\norder: 3\nsection: Repository\n---\n\n\n# Data Ingestion\n\nTo export activity logs for the current folder
\n\n 1. Navigate to any folder in the Repository (click on the  **Repository** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu) then navigate to a folder)\n\n 2. Click on the  button next to the current folder's breadcrumb\n\n 3. Click **Export Activities**\n\n 4. (Optional) In the popup dialog, select the start date from the **Since** field\n\n 5. (Optional) Select the desired output timezone from the **Timezone** dropdown menu\n\n 6. Click on the **Export CSV** button to download a CSV file. See [Activity Log File Format](#activity-log-export-format) for more details\n\n\n\nThere are several ways to upload images into the Repository. Depending on the desired workflow and volume of data to be ingested, use one of the following methods:\n\n- Upload files manually in a browser\n- Upload in bulk from a PC using the Upload Client software\n- Configure the image indexing service by contacting support\n- Upload through the API for customized workflows\n\n\n## Manual Uploads\n\nFiles can be manually uploaded into a folder using drag and drop or through a file selection dialog. Multiple images can be selected for upload using either method. The status of uploaded files will be indicated through a progress notification at the top of the screen as well as a progress bar on each new item in the [Folder Listing](/docs/repository/folder-listing/).\n\n
\n\n
\n\nTo upload file(s) using drag and drop
\n\n 1. Navigate to any folder in the Repository (click on the  **Repository** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu) then navigate to a folder)\n\n 2. Drag one or more files onto the folder listing area (until the \"Drop files to upload\" notification appears) then drop the files\n\n 3. To check upload status, click on the **Details** button from the upload progress notification at the top of the screen\n\n\n\n
\n\nTo upload file(s) using a file selection dialog
\n\n 1. Navigate to any folder in the Repository (click on the  **Repository** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu) then navigate to a folder)\n\n 2. Click on the  button at the top right of the item list\n\n 3. In the popup menu, click **Upload**\n\n 4. Click in the blue box to activate the file selection dialog or simply drag files into the blue box; repeat as required for other files\n\n 5. Click on the **Start Upload** button to start upload\n\n 6. Click on the **X** button to minimize the File Uploads dialog\n\n 7. To check upload status, click on the **Details** button from the upload progress notification at the top of the screen\n\n\n\n
\n\nTo check the status of recently uploaded files
\n\n 1. Look for the upload progress notification at the top of the screen\n\n 2. Click on the **Details** button on the notification\n\n\n\n
\n\nTo edit metadata for recently uploaded files
\n\n 1. Look for the upload progress notification at the top of the screen and, if it has not been dismissed, click on the **Details** button. If the notification has been dismissed, this method is not available and file metadata can be edited individually through the Repository listing\n\n 2. Click on the **Edit Metadata** button for any of the files listed\n\n 3. In the **Add fields** box look for the fields to be added or type a few letters to find the desired field; repeat as required for other fields\n\n 4. Edit the value in the provided field\n\n 5. Click on the **Save Changes** button to commit the field(s), or click on the **Cancel** button to discard changes\n\n 6. Click on the **X** button in the top right-hand corner of the File Uploads dialog\n\n\n\n
\n\nTo locate recently uploaded files
\n\n 1. Look for the upload progress notification at the top of the screen and, if it has not been dismissed, click on the **Details** button\n\n 2. Click on the  button below any of the recently uploaded files\n\n 3. Click on the **X** button in the top right-hand corner of the File Uploads dialog\n\n\n\n
\n\nTo clear the completed list of recently uploaded files
\n\n 1. Look for the upload progress notification at the top of the screen and, if it has not been dismissed, click on the **Details** button\n\n 2. Click on the **Clear Completed** button\n\n\n\n
\n\n### Multi-File Images\n\nTo upload multi-file images such as MRXS, NDPIS, AFI and VSI via the browser, the set of files and folders related to the image must be uploaded as a single archive file (e.g., a zip file). Do not include additional files or folders in the archive file or change the relative path of files in the archive (i.e., ensure the main file is at the root of the archive and there should be one image per archive).\n\nThe following archive formats are supported:\n- **tar**: Standard tarball archive format\n- **tar.gz**: gzip compressed tarball\n- **ZIP**: Created using the DEFLATE or DEFLATE64 algorithm. Microsoft Windows and macOS create these types of archives when a user sends files to a \"compressed folder\"\n\nThe following multi-file image formats are supported, with notes on how to properly organize the archive file contents.\n\nTo clear the upload progress history and remove it from view
\n\n 1. Look for the upload progress notification at the top of the screen\n\n 2. Click on the **Dismiss** button on the notification\n\n\n\n Refreshing the page while uploads are in progress will terminate in progress uploads and clear the list of recently uploaded files.\n
\n\n\n\n \n\n
\n\n3DHISTECH MRXS
\n\n An MRXS image consists of a base **.mrxs** image, and a correspondingly named folder which contains:\n\n - **Slidedat.ini**: Metadata for the entire image\n - **Index.dat**: Index describing how the data files are combined into a WSI\n - **DataXXXX.dat**: One or more image data files\n\n\n **Example**: An archive file named \"slide_001A.zip\" containing:\n\n ```\n slide_001A.mrxs\n slide_001A/\n Data0000.dat\n Data0001.dat\n ...\n Data0021.dat\n Data0022.dat\n Index.dat\n Slidedat.ini\n ```\n\n\n The scanner may not produce the .mrxs file, which is required by PathcoreFlow. CaseViewer will create this file if it does not already exist when it opens the image for viewing.\n
\n\n
\n\nAperio AFI
\n\n An AFI image consists of:\n\n - **IMAGE_NAME.afi**: An XML manifest of the files representing each channel\n - **\\*.svs**: One or more images, each representing a channel\n\n\n **Example**: An archive file named \"273481.zip\" containing:\n\n ```\n 273481_Alexa Fluor 488.svs\n 273481_Alexa Fluor 594.svs\n 273481_DAPI.svs\n 273481.afi\n ```\n\n\n\n
\n\nHamamatsu NDPIS
\n\n An NDPIS image consists of:\n\n - **IMAGE_NAME.ndpis**: An INI-like manifest of the files representing each channel\n - **\\*.ndpi**: One or more images, each representing a channel\n\n\n **Example**: An archive file named \"Ex_changer.tar.gz\" containing:\n\n ```\n Ex_changer-DAPI.ndpi\n Ex_changer-FITC.ndpi\n Ex_changer-TxRed.ndpi\n Ex_changer.ndpis\n ```\n\n\n\n
\n\nLunaphore OME-TIFF
\n\n An image in the Lunaphore variant of OME-TIFF can have an auxiliary XML file which defines the minimum value, maximum value, gamma value, and pseudocolor for each channel.\n This XML file needs to match the filename of the OME-TIFF file with \".xml\" appended.\n\n\n **Example**: An archive file named \"Lunaphore 10plex (5 cycles)_Slide 7_Annotation 1.tar\" containing:\n\n ```\n Lunaphore 10plex (5 cycles)_Slide 7_Annotation 1.ome.tiff\n Lunaphore 10plex (5 cycles)_Slide 7_Annotation 1.ome.tiff.xml\n ```\n\n\n\n
\n\nOlympus VSI
\n\n A VSI image consists of a base **.vsi** image, and a folder named **\\_IMAGE_NAME\\_** which can contain a variety of subfolders and files.\n\n **Example**: An archive file named \"Her2.tar\" containing:\n\n ```\n Her2.vsi\n _Her2_/\n stack1/\n frame_t.ets\n stack10001/\n frame_t.ets\n stack10004/\n frame_t.ets\n ```\n\n\n Only one image can be included in an archive file.\n
\n\n\n## Upload Client\n\nWhere the volume of images to be uploaded is large, it can be more efficient to upload images with a dedicated tool. The Pathcore Upload Client is a Windows application that has been designed for automating image uploads. It can be configured to upload images that appear in a \"watch\" folder. Once the images are uploaded, they are available for review in the [Unsorted Uploads](/docs/repository/unsorted-uploads/) section of the application, and from there they can be moved to the appropriate folder in the Repository.\n\nThe Upload Client can be configured to detect and upload images that are generated by a whole slide image scanner or it can be used to batch upload images on demand.\n\n\n Visit the Pathcore Help Center to download the Upload Client and learn more.\n
\n The Image indexing services add-on is required to enable this feature.\n
\n\nA side effect of the indexing service is the possibility in some circumstances for duplicate records to be created in the Repository. Images that are moved or copied on the storage system after they have been found by the indexing service will result in duplicate records, as the duplication will be detected by the service as a new file. This is not a huge problem, because both records will function normally (i.e., they will be viewable, no broken links, etc). However, the 2nd record won't have any of the annotations or metadata that may have been associated with the first record.\n\nTo reorganize the images in the Repository, we recommend using PathcoreFlow's built-in copy or move functions, which handle image metadata. Note that copy operations in the Repository are shallow, so the image data will not be duplicated on disk.\n\n\n## Custom Built Uploader\n\nUsers can develop custom upload workflows using the API, which provides methods for adding files and metadata to the Repository. Contact [Pathcore Support](mailto:support@pathcore.com) to learn more.\n","slug":"docs/repository/data-ingestion"},{"frontmatter":{"title":"Folder Listing","description":"folder listing"},"rawBody":"---\ntitle: Folder Listing\ndescription: folder listing\norder: 1\nsection: Repository\n---\n\n\n# Folder Listing\n\n\n\n## Folder Navigation\n\n
\n Depending on your Accessible Content settings, some folders may not be visible or accessible.\n
\n\n
\n\nTo navigate to a folder
\n\n 1. Click on the  **Repository** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu)\n\n 2. Navigate to a folder using the folders listing\n\n\n\n
\n\n\n## Current Folder\n\nWondering where you are? The path to the current folder is shown in a breadcrumb in the top bar of the Repository page. For example, **Repository > Folder > Subfolder**\n\nIf the breadcrumb exceeds a certain width, all of the folder names but the last are collapsed into an  ellipsis button. You can click on the ellipsis button to display the complete list of folders.\n\nTo create a new folder
\n\n 1. Click on the  button at the top right of the item list\n\n 2. In the popup menu, click **Create Folder**\n\n 3. Type a name for the new folder in the field\n\n 4. Click on the **Submit** button\n\n\n You can navigate to a parent folder by clicking into the breadcrumb.\n
\n\n\n### Current Folder Operations\n\nBy clicking the  button next to the current folder's name in the breadcrumb (near the top of the page) you can access a menu of operations to perform on the folder.\n\n\n Depending on your Permissions and add-ons some operations may not be available.\n
\n\n \n\n
\n\nMove
\n\n **Move** opens the Move Item dialog, allowing you to move this folder to any other accessible folder.\n\n 1. Click on the  button next to the current folder's breadcrumb\n\n 2. Click **Move**\n\n 3. In the popup dialog, select the destination folder from the available list\n\n 4. Click on the **Move to Folder** button\n\n\n\n If you attempt to move a folder which is governed by a reason for change tracking policy, you will be required to provide a reason for the change.\n
\n\n \n\n
\n\nCopy
\n\n **Copy** opens the Copy Item dialog, allowing you to make a copy of this folder in another folder.\n\n 1. Click on the  button next to the current folder's breadcrumb\n\n 2. Click **Copy**\n\n 3. In the popup dialog, select the destination folder from the available list\n\n 4. Click on the **Copy to Folder** button\n\n\n\n The new folder will be named \"Copy of folder name\".\n
\n\n
\n\nCopy URL
\n\n **Copy URL** copies the URL of the folder to the clipboard.\n\n\n\n
\n\nProperties
\n\n **Properties** displays the [Properties Dialog](/docs/repository/repository-operations/#properties-dialog) for this folder.\n\n\n\n \n\n
\n\nRename
\n\n **Rename** allows you to change the name of the current folder.\n\n 1. Click on the  button next to the current folder's breadcrumb\n\n 2. Click **Rename**\n\n 3. In the popup dialog, type a new name for the folder\n\n 4. Click on the **Rename** button or press the **Enter** key to save. To discard your changes, click on the **Cancel** button or press the **Escape** key\n\n\n\n If you attempt to rename a folder which is governed by a reason for change tracking policy, you will be required to provide a reason for the change.\n
\n\n \n\n
\n\nEdit Metadata
\n\n **Edit Metadata** opens a dialog where you can add, change, or remove [Metadata](/docs/metadata/) fields for the current folder.\n\n See the [Metadata](/docs/metadata/) section for more details.\n\n 1. Click on the  button next to the current folder's breadcrumb\n\n 2. Click **Edit Metadata**\n\n 3. The popup dialog allows you to add or remove metadata [System Fields](/docs/metadata/system-fields/), [Custom Fields](/docs/metadata/custom-fields/), and/or [Field Sets](/docs/metadata/field-sets/)\n\n\n\n If you attempt to modify a folder which is governed by a reason for change tracking policy, you will be required to provide a reason for the change.\n
\n\n
\n\nShare
\n\n **Share** opens the [Share Links](/docs/share-links/share-link-overview/) dialog, which allows you to add and manage share links for the current folder.\n\n See [Managing Share Links](/docs/share-links/managing-share-links/) for more details.\n\n 1. Click on the  button next to the current folder's breadcrumb\n\n 2. Click **Share**\n\n 3. The popup dialog allows you to add and manage share links\n\n\n\n A Share icon in the breadcrumb indicates share links are associated with the current folder.\n
\n\n\n\n
\n\nUpdate Fields [add-on]
\n\n See [Metadata - Synchronization](/docs/metadata/synchronization/).\n\n\n\n
\n\nUpdate Fields (Forced) [add-on]
\n\n See [Metadata - Synchronization](/docs/metadata/synchronization/).\n\n\n\n
\n\nMark as Read / Mark as Unread
\n\n An item can be marked as \"read\" or \"unread\" depending on whether or not you have previously viewed it.\n\n See [Read Status](/docs/repository/repository-operations/#read-status) for more details.\n\n 1. Click on the  button next to the current folder's breadcrumb\n\n 2. Click **Mark as Read** to enable the read status, or\n\n 3. Click **Mark as Unread** to clear the read status\n\n\n\n
\n\nFavorite / Unfavorite
\n\n **Favorite** tags the current folder as _Starred_. Items tagged this way are quickly and easily accessible from the Starred Items List.\n **Unfavorite** removes this tag.\n\n See [Favorite Status](/docs/repository/repository-operations/#favorite-status) for more details.\n\n 1. Click on the  button next to the current folder's breadcrumb\n\n 2. Click **Favorite** to add the _Starred_ tag, or\n\n 3. Click **Unfavorite** to remove the tag\n\n\n\n
\n\nDownload
\n\n **Download** opens the [Download](/docs/repository/repository-operations/#downloading) dialog, allowing you to save the contents and metadata locally.\n\n See [Downloading](/docs/repository/repository-operations/#downloading) for more details.\n\n 1. Click on the  button next to the current folder's breadcrumb\n\n 2. Click **Download**\n\n 3. In the popup dialog, select what you would like to download (files and/or metadata)\n\n 4. Click on the **Download** button\n\n\n\n
\n\nOpen in VIS [add-on]
\n\n **Open in VIS** allows you to open the current folder in Visiopharm.\n\n See [Visiopharm Integration](/docs/integrations/visiopharm-integration/) for more details.\n\n 1. Click on the  button next to the current folder's breadcrumb\n\n 2. Click **Open in VIS**\n\n 3. In the popup dialog, select your options\n\n 4. Click on the **Open** button\n\n\n\n
\n\nOpen in HALO [add-on]
\n\n **Open in HALO** allows you to open the current folder in Indica Labs's HALO software.\n\n See [HALO Integration](/docs/integrations/halo-integration/) for more details.\n\n 1. Click on the  button next to the current folder's breadcrumb\n\n 2. Click **Open in HALO**\n\n 3. A SIS file will download\n\n 4. Open the SIS file in HALO\n\n\n\n
\n\n\n## Name Filter\n\nThe list of items can be filtered by name for quicker browsing.\n\nExport Activities [add-on]
\n\n **Export Activities** opens the Export Activities dialog, which can generate a CSV file of changes made to the folder over a specified period of time.\n\n See [Activity Logs](/docs/repository/activity-logs/) for more details.\n\n 1. Click on the  button next to the current folder's breadcrumb\n\n 2. Click **Export Activities**\n\n 3. (Optional) In the popup dialog, select the start date from the **Since** field\n\n 4. (Optional) Select the desired output timezone from the **Timezone** dropdown menu\n\n 5. Click on the **Export CSV** button to download a CSV file\n\n\n\n \n\n
\n\n\n## Image Labels\n\nImage labels (sometimes called slide labels) can be shown in the Repository folder listing alongside an image's preview. Image labels are only displayed in [List View](#list-view) and [Icon View](#icon-view).\n\nTo filter the list
\n\n 1. Click in the  **Search** box above the list of items\n\n 2. Type in the filter you wish to apply to the names. Only the items matching this text will be displayed\n\n\n\n The filter can include one or more wildcard characters (
*) which matches any character zero or more times.\n \n\n
\n\n\n## Status\n\nA status icon is displayed next to an item's **Name** if there is something notable about that item. Hovering over the icon shows a tooltip with additional information.\n\nImages and attachments also have a **Status** [System Field](/docs/metadata/system-fields/) which describes the current status of the item within the Repository. The possible values for this field are \"Available\", \"Not Available\", and \"Missing\".\n\nThe status icon is only displayed in [List View](#list-view) and [Compact List View](#compact-list-view).\n\n| Icon | Tooltip | Status | Description |\n| :----: | :------- | :----- | :---------- |\n|  | File upload incomplete | Not Available | The file upload was incomplete |\n|  | File type detection failed | Not Available | PathcoreFlow was unable to determine what type of file this is |\n|  | File not ready for use | Not Available | Some other error has occurred with the file |\n|  | File missing | Missing | The underlying file data for this item is missing |\n|  | x Share Link(s) | Available | The number of Share Links associated with the item |\n\n\n## List View\n\nList View displays the content of a folder in a tabular format and you can sort the table using the available columns. Each column corresponds to a field.\n\nTo toggle image labels
\n\n 1. Navigate to any folder in the Repository (click on the  **Repository** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu) then navigate to a folder)\n\n 2. Click on the  button at the top right of the item list\n\n 3. Set the **Display labels in slide listings** toggle\n\n\n\n
\n\n\n### Sorting in List View\n\nList View arranges Repository items in a tabular fashion, making it convenient to display metadata and to sort the entries. In this mode, the columns of the table can be customized to show the Fields that are associated with each entry.\n\nTo enable List View
\n\n 1. Navigate to any folder in the Repository (click on the  **Repository** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu) then navigate to a folder)\n\n 2. Click on the **Display Mode** button at the top right of the item list. This button will appear different depending on the current display mode: List (), Compact List (), or Icon ()\n\n 3. In the popup menu, click **List**\n\n\n The table columns and sort order are automatically remembered.\n
\n\n\n\n
\n\nTo sort items in List View
\n\n 1. Navigate to any folder in the Repository (click on the  **Repository** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu) then navigate to a folder)\n\n 2. From the table header, click on a column until the desired sort order is shown (sort order is shown with  for ascending order and  for descending order in the table header adjacent to the selected column)\n\n\n\n
\n\nTo add a column
\n\n 1. Navigate to any folder in the Repository (click on the  **Repository** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu) then navigate to a folder)\n\n 2. Click on the  button at the top right of the item list\n\n 3. (Optional) Filter the available fields using the search box in the **Available Columns** section\n\n 4. Click on the  button next to a field in the **Available Columns** section\n\n 5. Click on the **Save** button\n\n\n\n
\n\nTo remove a column
\n\n 1. Navigate to any folder in the Repository (click on the  **Repository** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu) then navigate to a folder)\n\n 2. Click on the  button at the top right of the item list\n\n 3. Click on the  button next to a field in the **Visible Columns** section\n\n 4. Click on the **Save** button\n\n\n\n
\n\n\n### Image Thumbnail\n\nThe size of the preview image (thumbnail) is controlled by the **Row height** setting\n\nTo restore the default columns
\n\n 1. Navigate to any folder in the Repository (click on the  **Repository** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu) then navigate to a folder)\n\n 2. Click on the  button at the top right of the item list\n\n 3. Click on the **Restore Defaults** button at the bottom left of the popup dialog\n\n 4. Click on the **Save** button\n\n\n You can hover over the thumbnail with the cursor for a larger view\n
\n\n\n\n
\n\n\n## Compact List View\n\nCompact List View displays the content of a folder in a tabular format similar to List View, however image thumbnails are not shown and the rows are more compact. This allows you to see more entries at a time on a smaller display. You can still sort the table using the available columns. Each column corresponds to a field.\n\nTo change the Row Height
\n\n 1. Click on the  button at the top right of the item list\n\n 2. Use the slider to adjust **Row height** to the desired value\n\n 3. Click on the **Save** button\n\n\n\n
\n\n\n### Sorting in Compact List View\n\nSorting in Compact List View is the same as [sorting in List View](#sorting-in-list-view). See that section for more details.\n\n\n## Icon View\n\nIcon View displays the content of a folder as a series of icons. Icon View provides larger image thumbnails and labels, making it easier to preview image content. In this mode, metadata can only be seen for the selected item from the **Metadata** tab of the right-hand sidebar.\n\nTo enable Compact List View
\n\n 1. Navigate to any folder in the Repository (click on the  **Repository** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu) then navigate to a folder)\n\n 2. Click on the **Display Mode** button at the top right of the item list. This button will appear different depending on the current display mode: List (), Compact List (), or Icon ()\n\n 3. In the popup menu, click **Compact List**\n\n\n\n
\n\nTo enable Icon View
\n\n 1. Navigate to any folder in the Repository (click on the  **Repository** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu) then navigate to a folder)\n\n 2. Click on the **Display Mode** button at the top right of the item list. This button will appear different depending on the current display mode: List (), Compact List (), or Icon ()\n\n 3. In the popup menu, click **Icon**\n\n\n\n
\n\n\n### Sorting in Icon View\n\nThe folder items in Icon View can be sorted by item name, type, or last modified time.\n\nTo view metadata for an entry
\n\n 1. Navigate to any folder in the Repository (click on the  **Repository** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu) then navigate to a folder)\n\n 2. Select an entry by clicking on it\n\n 3. View associated metadata in the **Metadata** tab of the right-hand panel. You may need to click on the  button if the panel is collapsed\n\n\n\n
\n","slug":"docs/repository/folder-listing"},{"frontmatter":{"title":"","description":null},"rawBody":"---\nredirect: /docs/repository/repository-overview/\n---\n","slug":"docs/repository/"},{"frontmatter":{"title":"Repository Operations","description":"repository operations"},"rawBody":"---\ntitle: Repository Operations\ndescription: repository operations\norder: 2\nsection: Repository\n---\n\n\n# Repository Operations\n\nTo sort items in Icon View
\n\n 1. Navigate to any folder in the Repository (click on the  **Repository** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu) then navigate to a folder)\n\n 2. Click on the  button at the top right of the item list\n\n 3. Select the desired sort option from the **Sort By** dropdown menu: **Name**, **Type**, or **Last Modified**\n\n\n\nThis section contains a list of basic operations that are available for items in the Repository.\n\n
\n Different operations are available depending on the type and number of items selected.\n
\n\n\n## Context Menu\n\nMost operations can be performed via a context menu. This menu is accessed by right-clicking on an item in the [Folder Listing](/docs/repository/folder-listing/) (or one of the currently selected items when using [Multi-Select](#multi-select)). The same menu can be accessed by clicking the  button next to the item's name in the right-hand panel. You may need to click on the  button if the panel is collapsed.\n\n\n On a mobile device, tap and hold on an item to display the context menu. Alternatively, you may tap on an item to select it and then tap on the 1 Selected dropdown menu at the top of the item list, next to the search box.\n
\n\n
\n Depending on your Permissions and add-ons some operations may not be available.\n
\n\n \n\n
\n\nMove
\n\n **Move** opens the Move Item dialog, allowing you to move the item (or items) to any accessible folder.\n\n 1. Bring up the [context menu](#context-menu) for the item (or items)\n\n 2. Click **Move**\n\n 3. In the popup dialog, select the destination folder from the available list\n\n 4. Click on the **Move to Folder** button\n\n\n\n If you attempt to move an item which is governed by a reason for change tracking policy, you will be required to provide a reason for the change.\n
\n\n \n\n
\n\nCopy
\n\n **Copy** opens the Copy Item dialog, allowing you to make a copy of the item (or items) in another folder.\n\n\n When copying entries in the Repository, the underlying files are not duplicated (i.e., copies are linked to the same underlying file) and thus do not consume additional storage. However, the metadata associated with the copied entries, such as annotations, snapshots, and Custom Fields, are duplicated when an entry in the Repository is copied (i.e., duplicated entries will retain an independent copy of the original metadata).\n
\n\n 1. Bring up the [context menu](#context-menu) for the item (or items)\n\n 2. Click **Copy**\n\n 3. In the popup dialog, select the destination folder from the available list\n\n 4. Click on the **Copy to Folder** button\n\n\n \n The new file or folder will be named \"Copy of item name\".\n
\n\n
\n\nCopy URL — single item only
\n\n **Copy URL** copies the URL of the item to the clipboard.\n\n\n\n
\n\nOpen Folder — folders only
\n\n **Open Folder** navigates into the selected folder.\n\n\n\n
\n\nView Image(s) — images only
\n\n **View Images** opens the selected item (or items) in the [Viewer](/docs/viewer/overview/).\n\n\n Only images can be opened in the Viewer.\n
\n\n\n\n
\n\nProperties
\n\n **Properties** displays the [Properties Dialog](#properties-dialog) for the selected item (or items).\n\n\n\n
\n\nRetry Type Detection — attachments only
\n\n **Retry Type Detection** attempts to force the system to detect this attachment as an image again. This can be useful if an image uploaded completely, but for whatever reason is not being recognized by PathcoreFlow as an image. If this still does not work you may need to contact [Pathcore Support](mailto:support@pathcore.com).\n\n\n This operation only applies to attachments.\n
\n\n\n\n \n\n
\n\nRename — single item only
\n\n **Rename** allows you to change the name of the item.\n While all entries in the Repository have names, names do not have to be unique because each entry has a unique ID, see [Names and IDs](/docs/repository/repository-overview/#names-and-ids).\n\n\n It’s not possible to rename multiple items at the same time.\n
\n\n 1. Bring up the [context menu](#context-menu) for the item\n\n 2. Click **Rename**\n\n 3. In the popup dialog, type a new name for the item\n\n 4. Click on the **Rename** button or press the **Enter** key to save. To discard your changes, click on the **Cancel** button or press the **Escape** key\n\n\n \n If you attempt to rename an item which is governed by a reason for change tracking policy, you will be required to provide a reason for the change.\n
\n\n \n\n
\n\nEdit Metadata
\n\n **Edit Metadata** opens a dialog where you can add, change, or remove [Metadata](/docs/metadata/) fields for the item (or items).\n\n See the [Metadata](/docs/metadata/) section for more details.\n\n 1. Bring up the [context menu](#context-menu) for the item (or items)\n\n 2. Click **Edit Metadata**\n\n 3. The popup dialog allows you to add or remove metadata [System Fields](/docs/metadata/system-fields/), [Custom Fields](/docs/metadata/custom-fields/), and/or [Field Sets](/docs/metadata/field-sets/)\n\n\n\n If you attempt to modify an item which is governed by a reason for change tracking policy, you will be required to provide a reason for the change.\n
\n\n
\n\nShare — single item only
\n\n **Share** opens the [Share Links](/docs/share-links/share-link-overview/) dialog, which allows you to add and manage share links for the item.\n\n See [Managing Share Links](/docs/share-links/managing-share-links/) for more details.\n\n\n It’s not possible to share multiple items at a time. However it is possible to share a folder of items.\n
\n\n 1. Bring up the [context menu](#context-menu) for the item\n\n 2. Click **Share**\n\n 3. The popup dialog allows you to add and manage share links\n\n\n\n
\n\nUpdate Fields — single item only [add-on]
\n\n See [Metadata - Synchronization](/docs/metadata/synchronization/).\n\n\n\n
\n\nUpdate Fields (Forced) — single item only [add-on]
\n\n See [Metadata - Synchronization](/docs/metadata/synchronization/).\n\n\n\n
\n\nMark as Read / Mark as Unread
\n\n An item can be marked as \"read\" (name in plain text) or \"unread\" (name in bold) depending on whether or not you have previously viewed it.\n\n See [Read Status](#read-status) for more details.\n\n 1. Bring up the [context menu](#context-menu) for the item (or items)\n\n 2. Click **Mark as Read** to enable the read status, or\n\n 3. Click **Mark as Unread** to clear the read status\n\n\n\n
\n\nFavorite / Unfavorite
\n\n **Favorite** tags the item (or items) as _Starred_. Items tagged this way are quickly and easily accessible from the Starred Items List.\n **Unfavorite** removes this tag.\n\n See [Favorite Status](#favorite-status) for more details.\n\n 1. Bring up the [context menu](#context-menu) for the item (or items)\n\n 2. Click **Favorite** to add the _Starred_ tag, or\n\n 3. Click **Unfavorite** to remove the tag\n\n\n\n
\n\nDownload
\n\n **Download** opens the [Download](#downloading) dialog, allowing you to save items and metadata locally.\n\n See [Downloading](#downloading) for more details.\n\n 1. Bring up the [context menu](#context-menu) for the item (or items)\n\n 2. Click **Download**\n\n 3. In the popup dialog, select what you would like to download (files and/or metadata)\n\n 4. Click on the **Download** button\n\n\n\n
\n\nExport Figure — single Figure only
\n\n **Export Figure** opens the [Download Figure](/docs/viewer/figure-maker/#downloading-figures) dialog, allowing you to export a Figure as a common image format.\n\n\n\n
\n\nOpen in VIS [add-on]
\n\n **Open in VIS** allows you to open the item (or items) in Visiopharm.\n\n See [Visiopharm Integration](/docs/integrations/visiopharm-integration/) for more details.\n\n 1. Bring up the [context menu](#context-menu) for the item (or items)\n\n 2. Click **Open in VIS**\n\n 3. In the popup dialog, select your options\n\n 4. Click on the **Open** button\n\n\n\n When opening multiple images in Visiopharm, they must all be in the same folder. Also, no images in Unsorted Uploads can be opened in Visiopharm.\n
\n\n\n\n
\n\nOpen in HALO [add-on]
\n\n **Open in HALO** allows you to open the item (or items) in Indica Labs's HALO software.\n\n See [HALO Integration](/docs/integrations/halo-integration/) for more details.\n\n 1. Bring up the [context menu](#context-menu) for the item (or items)\n\n 2. Click **Open in HALO**\n\n 3. A SIS file will download\n\n 4. Open the SIS file in HALO\n\n\n\n
\n\nExport Activities — single item only [add-on]
\n\n **Export Activities** opens the Export Activities dialog, which can generate a CSV file of changes made to the item over a specified period of time.\n\n See [Activity Logs](/docs/repository/activity-logs/) for more details.\n\n 1. Bring up the [context menu](#context-menu) for the item\n\n 2. Click **Export Activities**\n\n 3. (Optional) In the popup dialog, select the start date from the **Since** field\n\n 4. (Optional) Select the desired output timezone from the **Timezone** dropdown menu\n\n 5. Click on the **Export CSV** button to download a CSV file\n\n\n\n \n\n
\n\n\n## Multi-Select\n\nOne or more files can be selected from the folder listing page in order to perform bulk operations such as download, copy or move.\n\nMove to Trash
\n\n **Move to Trash** allows you to move the selected item(s) to the [Trash](/docs/repository/trash/).\n\n 1. Bring up the [context menu](#context-menu) for the item (or items)\n\n 2. Click **Move to Trash**\n\n 3. Click on the **Yes** button to confirm if you are sure you wish to move the item(s) to the Trash. To cancel the action, click on the **Cancel** button or press the **Escape** key\n\n\n\n If you attempt to move an item which is governed by a reason for change tracking policy to Trash, you will be required to provide a reason for the change.\n
\n\n
\n\nTo select more than one file
\n\n 1. Navigate to any folder in the Repository (click on the  **Repository** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu) then navigate to a folder)\n\n 2. Click on an item from the file listing\n\n 3. While holding the **Ctrl** key (on Windows) or **⌘ / Command** key (on macOS) select another file\n\n 4. Repeat step 3 as necessary\n\n\n\n
\n\n\n## Description\n\nEvery item in the Repository has a user editable multi-line description. By default, an item's description is empty. Use the description to record a finding about an image, folder or file.\n\nTo select more than one file in a continuous range
\n\n 1. Navigate to any folder in the Repository (click on the  **Repository** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu) then navigate to a folder)\n\n 2. Click on the first item in the range from the file listing\n\n 3. While holding the **Shift** key, select the last file in the range\n\n\n\n \n\n
\n\n\n## Read Status\n\nThe names of items (files and folders) in the Repository are in bold to indicate an item is \"unread\". Once an item has been \"read\", plain text font is used for the name of the item. New items are always unread and are automatically marked as read once they have been opened, viewed or downloaded by a user. The following actions will cause the status of an item to be marked as \"read\":\n\n- Clicking on an image file causing the Viewer to launch\n- Clicking on any other item causing it open in the browser or be downloaded\n\nThe read status is unique for each user and can be toggled at any time, making it useful for tracking items that require further attention.\n\nTo edit an item's description
\n\n 1. Navigate to any folder in the Repository (click on the  **Repository** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu) then navigate to a folder)\n\n 2. Select a single item in a folder\n\n 3. Click on the **Edit Description** button (or **Add Description** button if no description yet exists) in the **Metadata** tab of the right-hand panel. You may need to click on the  button if the panel is collapsed\n\n 4. Type the description in the text area that appears\n\n 5. Click on the **Save** button to save the changes. To discard your changes, click on the **Cancel** button\n\n\n\n If you attempt to modify an item which is governed by a reason for change tracking policy, you will be required to provide a reason for the change.\n
\n The \"read\" status can be changed manually from the context menu for an item.\n
\n\n
\n\nTo view a list of all favorited items
\n\n 1. Click on the  **Starred** button in the **TAGS** section of the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu)\n\n\n\n
\n\n\n## Properties Dialog\n\nThe Properties dialog shows details about one or more Repository items.\n\nThe following details are displayed:\n- The name of a single item, or the total number of items\n - A  icon is displayed to the right of this field if at least one item has a share link. Hovering over the icon shows how many share links are associated with the item(s)\n- **Size**: the total estimated size to download the selected items and their children (e.g., image overlays, or folder contents)\n - Hovering over the  icon shows additional details such as how much of your Repository storage these items are using, or how much space can be recovered by deleting them\n- **Location**: The path in the Repository to the item (or items, if they are all in the same location)\n- **Contents**: The number and types of the items\n- **Created**: The creation date and time of an item (or items, if they are all within the same minute)\n- **Modified**: The last modified date and time of an item (or items, if they are all within the same minute)\n\nTo toggle favorite status
\n\n 1. Navigate to any folder in the Repository (click on the  **Repository** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu) then navigate to a folder)\n\n 2. Toggle the  button next to the item to indicate the status\n\n\n\n \n\n
\n\n## Downloading\n\nIn general, one or more files or folders can be downloaded from the Repository. Depending on the type and number of items downloaded, or the options selected in the download dialog, an archive file may need to be generated before the download can begin. The following will cause this to occur:\n- Selecting multiple items, or a folder of items, for download\n- Including metadata options in the download dialog\n- Downloading a [multi-file image format](/docs/repository/data-ingestion/#multi-file-images), such as MRXS\n\nWhen this is the case, the download dialog will include a dropdown menu to select an archive file format.\n\nCertain item types cannot be combined into a single download. For example, a Figure cannot be downloaded with any other item (including another Figure) because it has a unique export workflow.\n\nWhy are there three different sizes?
\n\n In some cases, the Properties dialog will show differing values for the total size, the size on disk, and the amount that would be recovered by deleting the selected item(s). This is because when entries in the Repository are copied, the underlying files are not duplicated (i.e., copies are linked to the same underlying file) and thus do not consume additional storage.\n\n - The size listed in the dialog represents the total size of the items (e.g., how much storage you would need on your local computer to download these items)\n\n - The space consumed on disk takes into account any copies (i.e., it only counts duplicates once)\n\n - The storage space recovered by deleting the selection also takes into account other copies of the items elsewhere in the Repository (e.g., deleting one copy of an item which still exists in another folder does not delete the underlying file)\n\n\n\n Example\n\n A user uploads an image of size 100 MiB to the Repository. They then make two copies of the image. The user selects two of these images and opens the Properties dialog.\n\n The Size reported will be 200 MiB. Hovering over the information icon shows a tooltip containing \"This selection consumes 100 MiB on disk. Deleting it would recover 0 B once the trash can is cleared.\"\n\n 200 MiB - the sum of the image files' sizes\n\n 100 MiB - because the two items are copies, there is only one underlying file\n\n 0 B - because there is still an active copy of the image in the Repository, deleting these items does not recover any storage space\n
\n Some web browsers may require your permission before downloading files.\n
\n\n\n\n \n\n
\n\n\n\nWhen the selection contains a single item, such as an image file, attachment, or report, the file itself will be downloaded. In other cases, such as for a single saved Figure item, the download will trigger an export and preview window. When there are multiple items or a folder selected, a downloadable archive will be generated in the chosen format with the option to include metadata.\n\n
\n\nDownload dialog options
\n\n The following options are available when downloading:\n\n - **Files**: Toggle to include the selected files and folders\n - **Metadata**: Toggle to include metadata about the selected files and folders. You can further customize the additional metadata to include:\n - **Annotations**: Toggle to include your private annotations as well as shared annotations by others\n - **Snapshot Coordinates**: Toggle to include snapshot coordinates and properties\n - **Fields**: Toggle to include [System Fields](/docs/metadata/system-fields/), [Custom Fields](/docs/metadata/custom-fields/), and [Field Sets](/docs/metadata/field-sets/). See the [Metadata](/docs/metadata/tags/) section for more details\n - **Tags**: Toggle to include tags you have assigned to the items\n - **Overlays**: Toggle to include overlay images added to images in the selected items\n - **VIS Results**: Toggle to include analysis results imported from Visiopharm. This option is only available if you have the [Visiopharm Integration](/docs/integrations/visiopharm-integration/) add-on\n - **HALO Results**: Toggle to include analysis results imported from HALO. This option is only available if you have the [HALO Integration](/docs/integrations/halo-integration/) add-on\n - **Download as JSON** / **Download as CSV**: choose the file format of the selected metadata. These options can only be selected if metadata is included in the download\n - **.tar**: This dropdown menu lets you select the archive format when more than one item and/or metadata are included\n\n\n The .tar.gz and .zip archive formats are not available by default in this release. If you require these formats, you may need to contact Pathcore Support.\n
\n\n
\n .tar archives are natively supported by Microsoft Windows 11, macOS, and all major Linux distributions. For users running Windows 10 or prior, we recommend a third-party archive manager such as [7-Zip](https://www.7-zip.org/).\n
\n\n
Protected Information->View (if slide label is enabled in the Figure) |\n | Image | Images->View
Images->Download
Protected Information->View |\n\n
\n\nUser restrictions
\n\n Certain permission flags are required to be able to download an item from the Repository. The permissions required depend on the type of item:\n\n | Item Type | Required Permission Flags |\n | --------- | ------------------------- |\n | Attachment | Files->View |\n | Figure | Images->ViewProtected Information->View (if slide label is enabled in the Figure) |\n | Image | Images->View
Images->Download
Protected Information->View |\n\n
\n Most downloads can be paused and resumed later (e.g., in the event of a network interruption).\n
\n","slug":"docs/repository/repository-operations"},{"frontmatter":{"title":"Repository Overview","description":"repository overview"},"rawBody":"---\ntitle: Repository Overview\ndescription: repository overview\norder: 0\nsection: Repository\n---\n\n\n# Repository Overview\n\n\n\n\n## A Virtual File System\n\nThe Repository is a virtual file system that is accessible from any internet-enabled device. It supports nested folders and all file types, like the file system on your computer, which is convenient for organizing and retaining your team's important files, images and related information.\n\n\n## Built-in Image Viewer\n\nAny of the [supported image formats](/docs/overview/supported-formats/#supported-image-formats), such as whole slide images, DICOM images and photos, can be viewed with the built-in image [Viewer](/docs/viewer/) on-demand, using streaming technologies. However, many of the non-image data files will need to be downloaded and viewed using external software.\n\n\n## Supported Metadata Types\n\nRepositories provide flexible and customizable methods for creating and tracking metadata. The following metadata types are supported at folder-level and file-level:\n\n- [Fields](/docs/metadata/system-fields/) (key-value pairs)\n- [Tags](/docs/metadata/tags/)\n\nAdditionally, for image files (i.e., files that have been identified as images) the following metadata types are also supported:\n\n- [Annotations](/docs/viewer/annotations-panel/)\n- [Snapshots](/docs/viewer/snapshots/)\n- [Overlays](/docs/viewer/overlays/)\n\n\n## Unlimited Folders\n\nFolders in the Repository can be nested to any depth and can contain all types of files. The top level of the Repository can only contain folders (i.e., no files) which is convenient for organizing and permissioning data for different users, groups, years, studies, etc.\n\n\n## Names and IDs\n\nWhile all entries in the Repository have names, names do not have to be unique because each entry has a unique ID. By convention, folders have integer IDs while files have alphanumeric IDs.\n\n\n## Navigation Menu\n\nThe navigation menu provides easy access to the various sections of the application, as well as a quick way to see all items with a given [tag](/docs/metadata/tags/).\n- In desktop mode, the navigation menu appears in the left-hand sidebar\n- On a mobile device, the navigation menu is accessed by tapping on the top left  button\n- In all modes, the sidebar can be collapsed with the  **Collapse Sidebar** button and expanded with the  button\n","slug":"docs/repository/repository-overview"},{"frontmatter":{"title":"Trash","description":"trash"},"rawBody":"---\ntitle: Trash\ndescription: trash\norder: 5\nsection: Repository\n---\n\n# Trash\n\n
\n\nThe Trash collects items that have been removed from the Repository and marked for deletion, but which have not yet been permanently erased. It provides a space to review and restore recently deleted items.\n\nBy default, items in the Trash are retained for 30 days. A different retention period can be set in the **Settings** under the [Team Customization](/docs/settings/team-customization/) tab, with some packages.\n\n
\n Access to the Trash requires at least one of the \"Folders->Delete\" or \"Files->Delete\" permission flags.\n
\n\n
\n\n\n## Trashed Items List\n\nThe list of items in the Trash is displayed using the same tabular interface as the Repository. The same table columns and sort order are also applied.\n\n- Instead of a **Location** column there is an **Original Location**, which indicates which folder contained the item before it was moved to the Trash\n - Hover over the **Original Location** value to see the full path\n- To change the view, sort order, or available columns, follow the same procedures as other [folders](/docs/repository/folder-listing/)\n\nTo access the Trash
\n\n 1. Click on the  **Trash** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu)\n\n\n A banner is displayed above the list of items indicating the current retention period set for items in the Trash.\n
\n\n\n## Context Menu\n\nMost operations can be performed via a context menu. This menu is accessed by right-clicking on an item in the search results listing (or one of the currently selected items when using [Multi-Select](/docs/repository/repository-operations/#multi-select)). The same menu can be accessed by clicking the  button next to the item's name in the right-hand panel. You may need to click on the  button if the panel is collapsed.\n\n\n On a mobile device, tap and hold on an item to display the context menu. Alternatively, you may tap on an item to select it and then tap on the 1 Selected dropdown menu at the top of the item list, next to the search box.\n
\n\n
\n The items displayed in the Trash are limited to those deleted from the current viewer's Accessible Content.\n
\n\n \n
\n\nTo restore an item (or items) to the Repository
\n\n 1. Click on the  **Trash** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu)\n\n 2. [Select one or more](/docs/repository/repository-operations/#multi-select) items to restore in the list\n\n 3. Bring up the [context menu](#context-menu) for the item (or items)\n\n 4. Click **Restore**\n\n 5. In the popup dialog, click on the **Restore** button to confirm. To cancel the action, click **Cancel** or press the **Escape** key\n\n 6. If the original location of one or more of the items is no longer available, you will be prompted to select a new folder for them:\n\n 1. In the popup dialog, select the destination folder from the available list\n\n 2. Click on the **Restore** button\n\n\n\n If you attempt to restore an item which was governed by a reason for change tracking policy when it was moved to the Trash, you will be required to provide a reason for the change.\n
\n\n
\n\nTo delete an item (or items) from the Trash
\n\n\n Items which are deleted forever cannot be recovered. Be careful with this action.\n
\n\n 1. Click on the  **Trash** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu)\n\n 2. [Select one or more](/docs/repository/repository-operations/#multi-select) items to delete in the list\n\n 3. Bring up the [context menu](#context-menu) for the item (or items)\n\n 4. Click **Delete Forever**\n\n 5. In the popup dialog, click on the **Delete Forever** button to confirm. To cancel the action, click **Cancel** or press the **Escape** key\n\n\n\n \n\n
\n","slug":"docs/repository/trash"},{"frontmatter":{"title":"","description":null},"rawBody":"---\nredirect: /docs/overview/supported-formats/\n---\n","slug":"docs/repository/supported-formats"},{"frontmatter":{"title":"Unsorted Uploads","description":"unsorted uploads"},"rawBody":"---\ntitle: Unsorted Uploads\ndescription: unsorted uploads\norder: 4\nsection: Repository\n---\n\n# Unsorted Uploads\n\nTo empty the Trash
\n\n When the Trash is emptied, all items within it are deleted forever.\n\n\n Items which are deleted forever cannot be recovered. Be careful with this action.\n
\n\n 1. Click on the  **Trash** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu)\n\n 2. Click on **Empty Trash** at the right-hand side of the banner above the list of items\n\n 3. In the popup dialog, click on the **Delete Forever** button to confirm. To cancel the action, click **Cancel** or press the **Escape** key\n\n\n \n Empty Trash requires the \"Files->Delete\" permission flag.\n
\n\nThis page is where all uploaded items that have yet to be sorted are displayed. These files are typically transferred into PathcoreFlow via the [Pathcore Upload Client](/docs/repository/data-ingestion/#upload-client).\n\n
\n Access to the Unsorted Uploads page requires the \"Manage uploaded files\" permission flag.\n
\n\n
\n\n\n## Uploads List\n\nThe list of items in Unsorted Uploads is displayed using the same tabular interface as the Repository. The same table columns and sort order are also applied.\n\n- To change the view, sort order, or available columns, follow the same procedures as other [folders](/docs/repository/folder-listing/)\n- Many of the Repository operations can be performed on items in the Unsorted Uploads list. See [Repository Operations](/docs/repository/repository-operations/) for more details\n","slug":"docs/repository/unsorted-uploads"},{"frontmatter":{"title":"Exporting Results","description":"exporting results"},"rawBody":"---\ntitle: Exporting Results\ndescription: exporting results\norder: 12\nsection: Search\n---\n\n\n# Exporting Results\n\nTo access the Unsorted Uploads page
\n\n 1. Click on the  **Uploads** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu)\n\n\n\nSearch results can be exported as a file in CSV format. The exported file will always contain one row per search result and the columns describe the [System Fields](/docs/metadata/system-fields/) and [Custom Fields](/docs/metadata/custom-fields/) associated with the results. For each row/result, the available columns are populated.\n\nThe first row in the file is a header row that defines the name of all fields associated with the exported results. The columns in the file represent the union of fields available for the exported results.\n\n
\n\n
\n\n\n## Empty Columns\n\nAn empty column in the exported file is somewhat ambiguous in that it may correspond to a field that is associated with the result but is undefined, or it may correspond to a field that is not associated with the result at all.\n","slug":"docs/search/exporting-results"},{"frontmatter":{"title":"Saved Searches","description":"saved searches"},"rawBody":"---\ntitle: Saved Searches\ndescription: saved searches\norder: 13\nsection: Search\n---\n\n\n# Saved Searches\n##### [BioPharma]\n\nSearch queries can be saved and recalled at the click of a button. Saving may be used for frequently used queries, for complex queries or for sharing a query with team members.\n\nA saved search query is not the same as saving the results of a search. When a saved query is executed, the results may vary depending on available data. To save the results of a search, [export search results](/docs/search/exporting-results/) after the search has been executed.\n\nTo export search results
\n\n 1. Click on the  **Search** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu)\n\n 2. Perform a search query. See [Basic Queries](/docs/search/search-overview/#basic-queries) for more details\n\n 3. Click on the  button at the top right of the search results\n\n 4. In the popup menu, click on **Export as CSV**\n\n 5. In the popup dialog, click on the **Start Export** button. If prompted, select a location to save the downloaded file\n\n\n\n
\n\nTo save a search query
\n\n 1. Click on the  **Search** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu)\n\n 2. Perform a search query. See [Basic Queries](/docs/search/search-overview/#basic-queries) for more details\n\n 3. Click on the **Save This Search** button\n\n 4. Type a name for the search conditions in the **Name** field\n\n 5. (Optional) Enable the **Share With Team** toggle to share this search with other users\n\n 6. Click on the **Save** button\n\n\n\n
\n\n\n## Sharing Saved Searches\n\nSaved searches can be shared with other users on the team. Once a saved search is shared, it will be visible to all other users on the team but other users cannot modify the saved search. Saved searches cannot be selectively shared.\n\nTo execute a previously saved search query
\n\n 1. Click on the  **Search** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu)\n\n 2. Click on the **Saved Searches** tab at the top of the page\n\n 3. Click on the search query you would like to execute\n\n\n\n
\n\n\n## Modifying Saved Searches\n\nSaved search queries cannot be directly modified but there is a simple workaround that involves executing a saved search, modifying the query, re-saving it as a new search and deleting the original query.\n\n\nTo share a saved search with your team
\n\n 1. Click on the  **Search** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu)\n\n 2. Click on the **Saved Searches** tab at the top of the page\n\n 3. Choose **Edit** from the **More** menu to the right of a saved search query in the list\n\n 4. Enable the **Share With Team** toggle\n\n 5. Click on the **Save** button\n\n\n\n
\n\nTo rename a saved search query
\n\n 1. Click on the  **Search** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu)\n\n 2. Click on the **Saved Searches** tab at the top of the page\n\n 3. Choose **Edit** from the **More** menu to the right of a saved search query in the list\n\n 4. Provide a new name\n\n 5. (Optional) adjust the **Share with Team** toggle\n\n 5. Click on the **Save** button\n\n\n\n
\n","slug":"docs/search/saved-searches"},{"frontmatter":{"title":"Search Operations","description":"search operations"},"rawBody":"---\ntitle: Search Operations\ndescription: search operations\norder: 11\nsection: Search\n---\n\n\n# Search Operations\n\nTo delete a saved search query
\n\n 1. Click on the  **Search** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu)\n\n 2. Click on the **Saved Searches** tab at the top of the page\n\n 3. Choose **Delete** from the **More** menu to the right of a saved search query in the list\n\n 4. Click on the **Yes** button to confirm deletion\n\n\n\nSearch can be used to perform bulk operations on the items in the Repository. All Repository operations can be performed with search results. See [Repository Operations](/docs/repository/repository-operations/) for more details.\n\n\n## Context Menu\n\nMost operations can be performed via a context menu. This menu is accessed by right-clicking on an item in the search results listing (or one of the currently selected items when using [Multi-Select](/docs/repository/repository-operations/#multi-select)). The same menu can be accessed by clicking the  button next to the item's name in the right-hand panel. You may need to click on the  button if the panel is collapsed.\n\n
\n On a mobile device, tap and hold on an item to display the context menu. Alternatively, you may tap on an item to select it and then tap on the 1 Selected dropdown menu at the top of the item list, next to the search box.\n
\n\n
\n Depending on your Permissions and add-ons some operations may not be available.\n
\n\n \n\n
\n\nMove
\n\n **Move** opens the Move Item dialog, allowing you to move the item (or items) to any accessible folder.\n\n 1. Bring up the [context menu](#context-menu) for the item (or items)\n\n 2. Click **Move**\n\n 3. In the popup dialog, select the destination folder from the available list\n\n 4. Click on the **Move to Folder** button\n\n\n\n If you attempt to move an item which is governed by a reason for change tracking policy, you will be required to provide a reason for the change.\n
\n\n \n\n
\n\nCopy
\n\n **Copy** opens the Copy Item dialog, allowing you to make a copy of the item (or items) in another folder.\n\n\n When copying entries in the Repository, the underlying files are not duplicated (i.e., copies are linked to the same underlying file) and thus do not consume additional storage. However, the metadata associated with the copied entries, such as annotations, snapshots, and Custom Fields, are duplicated when an entry in the Repository is copied (i.e., duplicated entries will retain an independent copy of the original metadata).\n
\n\n 1. Bring up the [context menu](#context-menu) for the item (or items)\n\n 2. Click **Copy**\n\n 3. In the popup dialog, select the destination folder from the available list\n\n 4. Click on the **Copy to Folder** button\n\n\n \n The new file or folder will be named \"Copy of item name\".\n
\n\n
\n\nCopy URL — single item only
\n\n **Copy URL** copies the URL of the item to the clipboard.\n\n\n\n
\n\nOpen Folder — folders only
\n\n **Open Folder** navigates into the selected folder.\n\n\n\n
\n\nView Image(s) — images only
\n\n **View Images** opens the select item (or items) in the [Viewer](/docs/viewer/overview/).\n\n\n Only images can be opened in the Viewer.\n
\n\n\n\n
\n\nProperties
\n\n **Properties** displays the [Properties Dialog](/docs/repository/repository-operations/#properties-dialog) for this folder.\n\n\n\n
\n\nRetry Type Detection — attachments only
\n\n **Retry Type Detection** attempts to force the system to detect this attachment as an image again. This can be useful if an image uploaded completely, but for whatever reason is not being recognized by PathcoreFlow as an image. If this still does not work you may need to contact [Pathcore Support](mailto:support@pathcore.com).\n\n\n This operation only applies to attachments.\n
\n\n\n\n \n\n
\n\nRename — single item only
\n\n **Rename** allows you to change the name of the item.\n While all entries in the Repository have names, names do not have to be unique because each entry has a unique ID, see [Names and IDs](/docs/repository/repository-overview/#names-and-ids).\n\n\n It’s not possible to rename multiple items at the same time.\n
\n\n 1. Bring up the [context menu](#context-menu) for the item\n\n 2. Click **Rename**\n\n 3. In the popup dialog, type a new name for the item\n\n 4. Click on the **Rename** button or press the **Enter** key to save. To discard your changes, click on the **Cancel** button or press the **Escape** key\n\n\n \n If you attempt to rename an item which is governed by a reason for change tracking policy, you will be required to provide a reason for the change.\n
\n\n \n\n
\n\nEdit Metadata
\n\n **Edit Metadata** opens a dialog where you can add, change, or remove [Metadata](/docs/metadata/) fields for the item (or items).\n\n See the [Metadata](/docs/metadata/) section for more details.\n\n 1. Bring up the [context menu](#context-menu) for the item (or items)\n\n 2. Click **Edit Metadata**\n\n 3. The popup dialog allows you to add or remove metadata [System Fields](/docs/metadata/system-fields/), [Custom Fields](/docs/metadata/custom-fields/), and/or [Field Sets](/docs/metadata/field-sets/)\n\n\n\n If you attempt to modify an item which is governed by a reason for change tracking policy, you will be required to provide a reason for the change.\n
\n\n
\n\nShare — single item only
\n\n **Share** opens the [Share Links](/docs/share-links/share-link-overview/) dialog, which allows you to add and manage share links for the item.\n\n See [Managing Share Links](/docs/share-links/managing-share-links/) for more details.\n\n\n It’s not possible to share multiple items at a time. However it is possible to share a folder of items.\n
\n\n 1. Bring up the [context menu](#context-menu) for the item\n\n 2. Click **Share**\n\n 3. The popup dialog allows you to add and manage share links\n\n\n\n
\n\nUpdate Fields — single item only [add-on]
\n\n See [Metadata - Synchronization](/docs/metadata/synchronization/).\n\n\n\n
\n\nUpdate Fields (Forced) — single item only [add-on]
\n\n See [Metadata - Synchronization](/docs/metadata/synchronization/).\n\n\n\n
\n\nMark as Read / Mark as Unread
\n\n An item can be marked as \"read\" (name in plain text) or \"unread\" (name in bold) depending on whether or not you have previously viewed it.\n\n See [Read Status](/docs/repository/repository-operations/#read-status) for more details.\n\n 1. Bring up the [context menu](#context-menu) for the item (or items)\n\n 2. Click **Mark as Read** to enable the read status, or\n\n 3. Click **Mark as Unread** to clear the read status\n\n\n\n
\n\nFavorite / Unfavorite
\n\n **Favorite** tags the item (or items) as _Starred_. Items tagged this way are quickly and easily accessible from the Starred Items List.\n **Unfavorite** removes this tag.\n\n See [Favorite Status](/docs/repository/repository-operations/#favorite-status) for more details.\n\n 1. Bring up the [context menu](#context-menu) for the item (or items)\n\n 2. Click **Favorite** to add the _Starred_ tag, or\n\n 3. Click **Unfavorite** to remove the tag\n\n\n\n
\n\nDownload
\n\n **Download** opens the [Download](/docs/repository/repository-operations/#downloading) dialog, allowing you to save items and metadata locally.\n\n See [Downloading](/docs/repository/repository-operations/#downloading) for more details.\n\n 1. Bring up the [context menu](#context-menu) for the item (or items)\n\n 2. Click **Download**\n\n 3. In the popup dialog, select what you would like to download (files and/or metadata)\n\n 4. Click on the **Download** button\n\n\n\n
\n\nOpen in VIS [add-on]
\n\n **Open in VIS** allows you to open the item (or items) in Visiopharm.\n\n See [Visiopharm Integration](/docs/integrations/visiopharm-integration/) for more details.\n\n 1. Bring up the [context menu](#context-menu) for the item (or items)\n\n 2. Click **Open in VIS**\n\n 3. In the popup dialog, select your options\n\n 4. Click on the **Open** button\n\n\n\n When opening multiple images in Visiopharm, they must all be in the same folder. Also, no images in Unsorted Uploads can be opened in Visiopharm.\n
\n\n\n\n
\n\nOpen in HALO [add-on]
\n\n **Open in HALO** allows you to open the item (or items) in Indica Labs's HALO software.\n\n See [HALO Integration](/docs/integrations/halo-integration/) for more details.\n\n 1. Bring up the [context menu](#context-menu) for the item (or items)\n\n 2. Click **Open in HALO**\n\n 3. A SIS file will download\n\n 4. Open the SIS file in HALO\n\n\n\n
\n\nExport Activities — single item only [add-on]
\n\n **Export Activities** opens the Export Activities dialog, which can generate a CSV file of changes made to the item over a specified period of time.\n\n See [Activity Logs](/docs/repository/activity-logs/) for more details.\n\n 1. Bring up the [context menu](#context-menu) for the item\n\n 2. Click **Export Activities**\n\n 3. (Optional) In the popup dialog, select the start date from the **Since** field\n\n 4. (Optional) Select the desired output timezone from the **Timezone** dropdown menu\n\n 5. Click on the **Export CSV** button to download a CSV file\n\n\n\n \n\n
\n\n\n## Exporting\n\nSearch results can be exported as a file in CSV format. See [Exporting Results](/docs/search/exporting-results/) for more details.\n\n\n## Tagging\n\nSearch results can be bulk tagged. This allows you to quickly apply a tag or set of tags to all items that match the search query.\n\nMove to Trash
\n\n **Move to Trash** allows you to move the selected item(s) to the [Trash](/docs/repository/trash/).\n\n 1. Bring up the [context menu](#context-menu) for the item (or items)\n\n 2. Click **Move to Trash**\n\n 3. Click on the **Yes** button to confirm if you are sure you wish to move the item(s) to the Trash. To cancel the action, click on the **Cancel** button or press the **Escape** key\n\n\n\n If you attempt to move an item which is governed by a reason for change tracking policy to Trash, you will be required to provide a reason for the change.\n
\n\n
\n","slug":"docs/search/search-operations"},{"frontmatter":{"title":"","description":null},"rawBody":"---\nredirect: /docs/search/search-overview/\n---\n","slug":"docs/search/"},{"frontmatter":{"title":"Accessible Content","description":"accessible content"},"rawBody":"---\ntitle: Accessible Content\ndescription: accessible content\norder: 42\nsection: Settings\n---\n\n\n# Accessible Content\n\n## General\n\nA user’s accessible content defines the set of folders that the user can access. These are the set of folders that a user will see in the system. Accessible content limitations are enforced in the Repository, in search, and via the API. Accessible content is related to [Data Groups](/docs/settings/data-groups/).\n\n## Granularity\n\nAccessible content for any user can be configured to include all folders in the Repository or restricted to an arbitrary set of folders in the Repository. A user may also be denied access to the Repository all together. To edit a user’s accessible content, see [Modifying Accessible Content](/docs/settings/user-management/#modifying-accessible-content).\n\n## Effect on Repository\n\nWhen entering the Repository, restricted users will only see folders allowed by their accessible content. Any folder that has been excluded from a user’s accessible content will simply not appear in the Repository. As a result, the Repository may look different for different users, especially at the top most level because it will only show the highest-level ancestor for the folder trees each user can access.\n\n## Special Considerations\n\nThough it’s possible to disallow access to the Repository for any user, there are side effects that make this not suitable for administrators in particular. Users that have no accessible content (i.e., do not have access to any folders) will experience some limitations, regardless of their permission level. For instance, the following capabilities will not be available for these users:\n\n- Cannot see or change the folders associated with groups in the Data Groups tab in Settings\n- Can set a user's Data Group during user creation and in the Edit Accessible Content menu option in the users table, but cannot see any folders for customizing access\n","slug":"docs/settings/accessible-content"},{"frontmatter":{"title":"Search Overview","description":"search overview"},"rawBody":"---\ntitle: Search Overview\ndescription: search overview\norder: 10\nsection: Search\n---\n\n\n# Search Overview\n\nTo apply tags to all search results
\n\n 1. Click on the  **Search** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu)\n\n 2. Perform a search query. See [Basic Queries](/docs/search/search-overview/#basic-queries) for more details\n\n 3. Click on the  button at the top right of the search results\n\n 4. In the popup menu, click on **Tag All Results**\n\n 5. In the popup dialog, choose a tag from the **Add a tag..** dropdown menu. To create a new tag, type directly into the field and click on the **+ New tag** option\n\n 6. Click on the **Tag Results** button\n\n\n\nSearch can be used for finding files and folders based in the Repository. Search uses a versatile query language that can be used to create complex expressions. Search queries can be quite specific with support for various advanced features:\n\n- One or more conditions\n- Condition groups (i.e., brackets are supported)\n- Restricting results to a folder or set of folders\n- Restricting result type (e.g., image, folders, files, etc.)\n\n\n## Quick Search\n\nClicking on a  icon next to a [Custom Field](/docs/metadata/custom-fields/) value anywhere will trigger a search for all items in the Repository that have a field with the same value that was clicked. The search can then be modified to a different value for the same field from the search page.\n\n\n## Search Preambles\n\nSearch queries have preambles that can be used to narrow the search results:\n\n- The results type preamble may be used to narrow the types of items returned\n- The location preamble may be used to narrow the folders that are searched\n\n
\n\n
\n\nTo set the result type preamble
\n\n 1. Click on the  **Search** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu)\n\n 2. Choose one or more types from the **Find** dropdown menu\n\n\n\n
\n\n\n## Basic Queries\n\nTo search for a file or folder in the Repository, start by creating a search query. The search query can reference some of the built-in [System Fields](/docs/metadata/system-fields/) as well as any user-defined [Custom Fields](/docs/metadata/custom-fields/).\n\nTo set the location preamble
\n\n 1. Click on the  **Search** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu)\n\n 2. Click on the  icon and choose the set of folders for the search\n\n 3. Click on the **X** button when done and continue building the search query\n\n\n\n
\n\n\n## Advanced Queries\n\nAdvanced search can be fully customized and may include logical groups (i.e., bracketed expressions).\n\nTo create a basic search query
\n\n 1. Click on the  **Search** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu)\n\n 2. (Optional) Configure the [result type preamble](#search-preambles) from the **Find** dropdown menu\n\n 3. (Optional) Configure the [location preamble](#search-preambles) from the  dropdown menu\n\n 4. (Optional) Configure the logical operator from the **Matching** dropdown menu\n\n 5. Click on the **+ Condition** button; repeat as necessary\n\n a. Select a field from the dropdown menu\n\n b. Select an operation\n\n c. Fill the field accordingly\n\n 6. Click on the **Search** button to run the query\n\n Search results will be displayed on the same page\n\n\n\n
\n","slug":"docs/search/search-overview"},{"frontmatter":{"title":"","description":null},"rawBody":"---\nredirect: /docs/settings/my-account/\n---\n","slug":"docs/settings/"},{"frontmatter":{"title":"My Account","description":"my account"},"rawBody":"---\ntitle: My Account\ndescription: my account\norder: 38\nsection: Settings\n---\n\n\n# My Account\n\nTo create an advanced search query
\n\n 1. Click on the  **Search** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu)\n\n 2. (Optional) Configure the [result type preamble](#search-preambles) from the **Find** dropdown menu\n\n 3. (Optional) Configure the [location preamble](#search-preambles) from the  dropdown menu\n\n 4. (Optional) Configure the logical operator from the **Matching** dropdown menu\n\n 5. Click on the **+ Condition** button; repeat as necessary\n\n a. Select a field from the dropdown menu\n\n b. Select an operation\n\n c. Fill the field accordingly\n\n 6. (Optional) Click **+ Condition Group**; repeat as necessary\n\n a. Repeat step 5 as necessary\n\n 7. Click on the **Search** button to run the query\n\n Search results will be displayed on the same page\n\n\n\nMany of the restrictions that govern user accounts, such as accessible content (i.e., the files and folders visible in the Repository), roles and permissions (i.e., the actions you can take with the files in the Repository), as well as the ability to modify properties of Custom Fields and report templates, are controlled by your account administrator. Contact your administrator if you have any questions about these topics.\n\n\n## User Profile\n\nUsers can modify certain account properties and preferences such as their name, profile photo and signature. Users cannot change their email address.\n\n
\n\n
\n\nTo change the name of your account
\n\n 1. Click on the user icon at the top right of the screen\n\n 2. In the popup menu, click on **My Account**\n\n 3. Click on the Profile tab if necessary\n\n 4. Click on the **Edit** button in the Name section\n\n 5. Edit the text in the textbox\n\n 6. Click on the **Apply** button to save your changes\n\n\n\n
\n\nTo add or change the profile photo of your account
\n\n 1. Click on the user icon at the top right of the screen\n\n 2. In the popup menu, click on **My Account**\n\n 3. Click on the Profile tab if necessary\n\n 4. Click on the current profile photo, or the **Edit** button in the Profile Photo section\n\n 5. Click on **Upload Photo** and select an image from your computer\n\n 6. (Optional) Use the slider beneath the image to adjust the visible content\n\n 7. Click on the **Apply** button to save your changes, or **Cancel** to discard them\n\n\n\n
\n\nTo add or change the signature image for your account
\n\n 1. Click on the user icon at the top right of the screen\n\n 2. In the popup menu, click on **My Account**\n\n 3. Click on the Profile tab if necessary\n\n 4. Click on the **Edit** button to in the Signature section\n\n 5. Click on the **Upload Signature** button and select an image from your PC\n\n 6. Click on the **Apply** button to save your changes\n\n\n\n
\n\n\n## Preferences\n\n### Visiopharm Preferences [add-on]\n\nTo change your password
\n\n 1. Click on the user icon at the top right of the screen\n\n 2. In the popup menu, click on **My Account**\n\n 3. Click on the Profile tab if necessary\n\n 4. Click on **Change Password**\n\n 5. Enter your current password\n\n 6. Enter a new password\n\n 7. Renter the new password to confirm\n\n 8. Click on the **Apply** button to save your changes\n\n\n\n
\n\nTo change the default application used with the Open in VIS button
\n\n 1. Click on the user icon at the top right of the screen\n\n 2. In the popup menu, click on **My Account**\n\n 3. Click on the Preferences tab\n\n 4. Under the Visiopharm section, locate the **Default Application** setting\n\n 5. Select either _VIS_ or _VIS Basic_, depending on which software you have installed\n\n\n\n \n\n
\n\n\n## Teams\n\nA user may be a member of more than one team within PathcoreFlow. Each team has its own [Repository](/docs/repository/), as well as associated [Data Groups](/docs/settings/data-groups/) and [Roles](/docs/settings/roles/).\n\nTo change the sub-image handling behavior
\n\n 1. Click on the user icon at the top right of the screen\n\n 2. In the popup menu, click on **My Account**\n\n 3. Click on the Preferences tab\n\n 4. Under the Visiopharm section, locate the **Sub-image Handling** setting\n\n 5. Select either _All Sub-images_ or _First Sub-image_\n\n\n\n All Sub-images is only supported in versions of Visiopharm released after Q2 2022.\n
\n A user can only be logged into one team at a time.\n
\n\n\n \n\n
\n\n\n## Forgotten Password\n\nIn the case a user forgets their password, they can use the self-serve option to reset it.\n\nTo switch your currently active team
\n\n 1. Click on the user icon at the top right of the screen\n\n 2. Under **Other Teams** select the name of the team to which you want to switch. Your current team is indicated with a check mark\n\n\n\n Other Teams will only appear in the popup menu if the user is part of more than one team.\n
\n Users on a team with SSO enforced cannot reset their password in PathcoreFlow and should instead contact their team administrator.\n
\n\n
\n","slug":"docs/settings/my-account"},{"frontmatter":{"title":"Data Groups","description":"data groups"},"rawBody":"---\ntitle: Data Groups\ndescription: data groups\norder: 43\nsection: Settings\n---\n\n\n# Data Groups\n\nTo reset a forgotten password
\n\n 1. Visit the login page for your PathcoreFlow service\n\n 2. Enter your email address in the **Email** field\n\n 3. Click on the **Log in with password** link below the login form\n\n 4. Click on the **Reset password** link below the login form\n\n 5. Enter your email address in the **Email** field\n\n 4. Click on the **Submit** button\n\n 5. Follow the instructions in the email message to reset the password\n\n\n\nData Groups can be used to control the accessible content of several users such as specific teams at once. When a user is assigned a data group, they inherit all accessible content from it. Any updates to the data group's accessible content will update the accessible content of users with that data group as well.\n\nTo assign data groups, see [Modifying Accessible Content](/docs/settings/user-management/#modifying-accessible-content).\n\n\n## Creating Data Groups\n\nCreate a data group for user types that need limited access to the content in the Repository. The data group can be used to define a set of folders and can be assigned to the appropriate users.\n\n
\n\n
\n\n\n## Modifying Data Groups\n\nModifying a data group immediately affects all users that are associated with it.\n\nTo create a data group
\n\n 1. Click on the  **Settings** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu)\n\n 2. Click on the **Data Groups** tab\n\n 3. Click on the **New Data Group** button\n\n 4. Type in a name for the data group under the **Data Group Name** field\n\n 5. Select accessible folders under the **Access Grants** section\n\n 6. Click on the **Save** button\n\n\n\n
\n\n\n## Deleting Data Groups\n\nData groups can only be deleted if they are not associated with any user. Before deleting a data group, ensure its user associations are cleared. See [Modifying Accessible Content](/docs/settings/user-management/#modifying-accessible-content) for more details.\n\nTo modify a data group
\n\n 1. Click on the  **Settings** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu)\n\n 2. Click on the **Data Groups** tab\n\n 3. Select a data group to edit\n\n 4. Click on the **Edit Data Group** button\n\n 5. (Optional) Type in a new name for the data group under the **Data Group Name** field\n\n 6. (Optional) Select accessible folders under the **Access Grants** section\n\n 7. Click on the **Save** button\n\n\n\n
\n","slug":"docs/settings/data-groups"},{"frontmatter":{"title":"Permissions","description":"permissions"},"rawBody":"---\ntitle: Permissions\ndescription: permissions\norder: 40\nsection: Settings\n---\n\n\n# Permissions\n\nTo delete a data group
\n\n 1. Click on the  **Settings** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu)\n\n 2. Click on the **Data Groups** tab\n\n 3. Select a data group to delete\n\n 4. Click on the **Delete** button\n\n 5. Click on the **Yes** button to confirm\n\n\n\nPermissions define the set of actions that users can perform with the data that is accessible to them (e.g., download, edit, view).\n\n\n## Permission Flags\n\nUser permissions are achieved through a set of fine-grained flags that team administrators can use to manage what actions users can perform with the data they can access. Permissions are divided into several categories of privileges that span actions at team level, image level, folder level, and file level.\n\n
\n All entries in the Repository that are detected as a supported image format are treated as an \"Image\" type and have dedicated permissions flags. All other entries in the Repository (e.g., reports, Figures, attachments) are treated as \"Files\" and also have dedicated permissions.\n
\n\n\n### Team Permissions\n\nThe following flags govern team administration.\n\n| Flag | Description |\n| ----------------------- | ------------------------------------------------------------ |\n| Manage users | Allows a user to view, edit, create or delete [Users](/docs/settings/user-management/). |\n| Manage roles | Allows a user to view, edit, create or delete [Data Groups](/docs/settings/data-groups/) and [Roles](/docs/settings/roles/). |\n| Manage fields | Allows a user to view, edit, create or delete [Fields](/docs/metadata/system-fields/) and [Field Sets](/docs/metadata/field-sets/). |\n| Manage report templates | Allows a user to view, edit, create or delete [Report Templates](/docs/report-templates/report-templates-overview/). |\n| Manage assignment rules | Allows a user to view, edit, create or delete assignment rules for cases. |\n| Manage uploaded files | Allows a user to view or create unsorted uploads. |\n| Manage team | Allows a user to edit the [Team Settings](/docs/settings/team-customization/). |\n| Export activities | Allows a user to export detailed [Activity Logs](/docs/repository/activity-logs/). |\n| Preview activities | Allows a user to access the Activities tab. |\n| Manage policies | Allows a user to view, edit, create or delete [policies](/docs/settings/policies/). |\n\n\n### Image Permissions\n\nThe following flags govern all entries in the Repository that are detected as a supported image format. The entries are treated as images and given the Image type.\n\n| Flag | Description |\n| -------------------------- | ------------------------------------------------------------ |\n| View | Allows a user to view an image and its metadata including fields, snapshots, overlays. |\n| View shared annotations | Allows a user to view shared annotations on an image to which they have access. |\n| Create shared annotations | Allows a user to create and delete shared annotations and change the state of a private annotation, which the user has created, to shared. |\n| Create private annotations | Allows a user to create private annotations. |\n| Download | Allows a user to download an image or attachment. |\n| Edit metadata | Allows a user to:- Edit image metadata fields
- Edit image description
- Edit, create, or delete image overlays
- Edit, create, or delete image snapshots
- Edit or delete any user’s shared annotations
- Set default image rotation |\n| Manage share links | Allows a user to edit, create, or delete share links for images. |\n| View shared image settings | Allows a user to save private image settings and see collections of image settings shared by other members of their team. |\n| Share image settings | Allows a user to share image settings with the rest of their team.
\"View shared image settings\" is a prerequisite for this permission, and it does not appear until that permission is granted. |\n| Manage image settings | Allows a user to change the preferred and shared status of all image settings for their team.
\"Share image settings\" is a prerequisite for this permission, and it does not appear until that permission is granted. |\n\n\n### Folder Permissions\n\nThe following flags govern folders in the Repository and/or Cases in the Dashboard.\n\n| Flag | Description |\n| ------------------ | ------------------------------------------------------------ |\n| View | Allows a user to view the Repository and its folders, and cases. |\n| Create | Allows a user to create folders and cases. |\n| Edit metadata | Allows a user to edit folder-level Fields and case reports. |\n| Manage share links | Allows a user to edit, create or delete share links for folders. |\n| Delete | Allows a user to delete folders. |\n\n\n### File Permissions\n\nThe following flags govern all entries in the Repository that are not detected as an image (e.g., reports, Figures, attachments). The entries are treated as files and have dedicated permissions.\n\n| Flag | Description |\n| ------------------ | ------------------------------------------------------------ |\n| View | Allows a user to view attachments, snapshots, reports and report templates. |\n| Upload | Allows a user to upload files, generate reports and link DICOM resources from a connected PACS into folders. |\n| Edit metadata | Allows a user to edit Fields for non-image files and reports, and run type detection on a file. |\n| Manage share links | Allows a user to edit, create, or delete share links for non-image files. |\n| Delete | Allows a user to delete all files (including image files). |\n\n\n### Protected Information (PI) Flags\n\nThe following flags govern metadata Fields.\n\n| Flag | Description |\n| -------- | ------------------------------------------------------------ |\n| View | Allows a user to view field values that have been marked with the Protected Information (PI) flag and slide labels. |\n","slug":"docs/settings/permissions"},{"frontmatter":{"title":"Policies","description":"policies"},"rawBody":"---\ntitle: Policies\ndescription: policies\norder: 47\nsection: Settings\n---\n\n\n# Policies\n##### [add-on]\n\nPolicies may be used to control when and where certain features apply to a user's actions. For example, a policy could be defined which requires users to provide a reason when they change any metadata associated with images in a specific subfolder.\n\n
\n The Reason for change tracking add-on and \"Manage policies\" permission flag is required to create or edit policies.\n
\n\n\n\n
\n\nTo view the list of configured policies
\n\n 1. Click on the  **Settings** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu)\n\n 2. Click on the **Policies** tab\n\n\n\n
\n\nTo sort the policy list
\n\n 1. Click on the  **Settings** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu)\n\n 2. Click on the **Policies** tab\n\n 3. From the table header, click on a column until the desired sort order is shown (sort order is shown with  for ascending order and  for descending order in the table header adjacent to the selected column)\n\n\n\n
\n\nTo enable or disable a policy
\n\n 1. Click on the  **Settings** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu)\n\n 2. Click on the **Policies** tab\n\n 3. Set the **Active** toggle next to the policy's name\n\n\n\n
\n\n## Reason for Change Tracking\n\nWhen **reason for change tracking** is enabled, users are prompted to input a reason for any change made to an item in the Repository or Viewer. Policies provide the ability to fine-tune when and where reason for change tracking is required for the team. This feature was designed to allow both GLP (Good Laboratory Practice) and non-GLP studies to be run within the same team without disrupting the existing folder structure.\n\nTo delete a policy
\n\n 1. Click on the  **Settings** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu)\n\n 2. Click on the **Policies** tab\n\n 3. Select one or more policies from the table by holding the **Ctrl** key (on Windows) or **⌘ / Command** key (on macOS) key and clicking on them\n\n 4. Bring up the context menu for the policy (or policies)\n\n 5. Click **Delete**\n\n 6. Click on the **Yes** button to confirm\n\n\n\n
\n\nTo create a reason for change tracking policy
\n\n 1. Click on the  **Settings** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu)\n\n 2. Click on the **Policies** tab\n\n 3. Click on the **Add Repository Policy** button\n\n 4. Type a name for the policy in the **Policy name** field\n\n 5. Click on the  button next to **Folders Tracked**\n 1. In the popup dialog, set the **Apply tracking to all folders in the repository** toggle (only appears if no other policies exist)\n 2. Select the Repository folders to which this policy will apply, if the above toggle was disabled or other policies already exist\n 3. Click on the **Apply** button\n\n 6. Click on the  button next to **Data Types**\n 1. In the popup dialog, set the toggle for the data types that will require a reason for change. The default is to enable all data types\n 2. Click on the **Apply** button\n\n 7. Click on the **Create Policy** button\n\n\n\n Only folders that are not already the target of a reason for change tracking policy may be selected for a new policy.\n
\n\n\n\n
\n","slug":"docs/settings/policies"},{"frontmatter":{"title":"Roles","description":"roles"},"rawBody":"---\ntitle: Roles\ndescription: roles\norder: 41\nsection: Settings\n---\n\n\n# Roles\n\nTo edit a reason for change tracking policy
\n\n 1. Click on the  **Settings** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu)\n\n 2. Click on the **Policies** tab\n\n 3. Bring up the context menu for a policy\n\n 4. Click **Edit**\n\n 5. (Optional) Type a new name for the policy in the **Policy name** field\n\n 6. (Optional) Click on the  button next to **Folders Tracked**\n 1. In the popup dialog, select the Repository folders to which this policy will apply\n 2. Click on the **Apply** button\n\n 7. (Optional) Click on the  button next to **Data Types**\n 1. In the popup dialog, set the toggle for the data types that will require a reason for change. The default is to enable all data types\n 2. Click on the **Apply** button\n\n 8. Click on the **Save Policy** button\n\n\n\nWhile the permissions assigned to each user can be customized on a user-by-user basis, it’s convenient to use roles for expressing the collection of permissions for different user types (e.g., viewers, editors, administrators). Roles are a convenient shorthand for defining and assigning permissions to users.\n\n\n## System Roles\n\nThere are a number of roles that are predefined in the system. These roles cannot be modified and are always available. The predefined roles are as follows:\n\n- **Administrator**: has all possible permissions\n- **Editor**: has all permissions except for the ability to manage team-level settings, plus the ability to preview activities\n- **Viewer**: has permissions to view and download files and metadata but cannot edit or delete any data\n- **Anonymized Viewer**: has all the permissions of the Viewer except they cannot view PI, download items, or preview activities\n\n
\n\n
\n\n\n## Custom Roles\n##### [BioPharma]\n\nTo complement the builtin System Roles, you may need to create additional roles. A major benefit of custom Roles comes from inheritance; changes made to a role are inherited by all users that are associated with the role. In this sense, custom roles allow administrators to control the permissions of several users at once.\n\nTo view system roles
\n\n 1. Click on the  **Settings** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu)\n\n 2. Click on the **Roles** tab\n\n 3. Look for Yes in the **System Role?** column of the roles table\n\n\n\n
\n\n\n### Editing Custom Roles\n\nEditing roles is a convenient way to modify the permission of all users that are associated with a particular role. For this reason, use caution when editing roles.\n\nTo create a new custom role
\n\n 1. Click on the  **Settings** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu)\n\n 2. Click on the **Roles** tab\n\n 3. Click on the **New Role** button\n\n 4. Type a name for the new role in the **Role Name** field\n\n 5. Select [Permission Flags](/docs/settings/permissions/#permission-flags) for the new role\n\n 6. Click on the **Save** button\n\n\n System roles cannot be modified.\n
\n\n\n\n
\n\n\n### Deleting Custom Roles\n\nWhen a role is deleted, all the users associated with the role retain the permissions they had before the role was deleted. All users that were associated with the deleted role became users with custom permissions.\n\nTo edit a non-system role
\n\n 1. Click on the  **Settings** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu)\n\n 2. Click on the **Roles** tab\n\n 3. Select a role from the table\n\n 4. Click on the **Edit Role** button above the table\n\n 5. Modify the role’s properties\n 1. Edit the role’s name\n 2. Modify the associated [Permission Flags](/docs/settings/permissions/#permission-flags)\n\n 6. Click on the **Save** button\n\n\n System roles cannot be deleted.\n
\n\n\n\n
\n","slug":"docs/settings/roles"},{"frontmatter":{"title":"","description":null},"rawBody":"---\nredirect: /docs/settings/saml-sso/\n---\n","slug":"docs/settings/saml-single-sign-on"},{"frontmatter":{"title":"SAML SSO","description":"saml sso"},"rawBody":"---\ntitle: SAML SSO\ndescription: saml sso\norder: 46\nsection: Settings\n---\n\n\n# SAML SSO\n##### [add-on]\n\nSecurity Assertion Markup Language, or SAML, can be configured as an option for authenticating users. This allows an organization to set up users in a single, centralized place and manage their access to multiple applications. Users only have to remember a single set of credentials across the systems they use. Administrators can enforce their desired password policies at the SAML identity provider, and many providers support additional security features such as multi-factor authentication (MFA).\n\nTo delete a non-system role
\n\n 1. Click on the  **Settings** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu)\n\n 2. Click on the **Roles** tab\n\n 3. Select a role from the table\n\n 4. Click on the **Delete** button above the table\n\n 5. Click on the **Yes** button to confirm\n\n\n The SAML SSO add-on and \"Manage team\" permission flag is required to view and change the SAML SSO configuration.\n
\n\n\n## SP Details\n\nThe SP Details form provides the information needed to configure SAML SSO with your identity provider. It also provides an easy way to copy these values for use in setting up your SAML single sign-on. These values cannot be altered via this form.\n\n- **Entity ID**: The unique ID used by your identity provider to identify your PathcoreFlow team\n- **Assertion Consumer Service URL**: The URL used by the identity provider to send the SAML assertion. This is sometimes also called a \"Reply URL\"\n- **Name ID Format**: The format of the user identifier expected by PathcoreFlow in responses from the identity provider. The only format that is accepted is email address\n\n\n\n
\n\n\n## IdP Details\n\nIn order to enable SSO, an identity provider must be configured in PathcoreFlow by a team administrator.\n\n- **Entity ID**: This is a unique identifier for your configured SSO application at the identity provider\n- **Single Sign On URL**: The URL at the identity provider where users are redirected to complete the log in\n- **Certificate**: A public key provided by your identity provider in either PEM or DER format\n\nTo view the SAML service provider (SP) details
\n\n 1. Click on the  **Settings** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu)\n\n 2. Click on the **SAML SSO** tab\n\n 3. Review the values in the [SP Details](#sp-details) section\n\n 4. (Optional) Click on the  button to the right of a field to copy its contents to the clipboard\n\n\n Only one identity provider can be configured for a team at a time.\n
\n\n\n\n
\n The \"email\" attribute sent from the identity provider is used to match a user account by their email address set in PathcoreFlow. These values must match.\n\n The \"name\" attribute sent from the IdP is used to update an account's display name.\n
\n\nInstructions for external providers are provided for convenience. If you require assistance in setting up the SAML identity provider, please contact the support for that provider.\n\n\n\n
\n\nTo configure Google Workspace as your identity provider
\n\n\n The user setting up SAML SSO must also be an active user in Google Workspace.\n
\n\n 1. Click on the  **Settings** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu)\n\n 2. Click on the **SAML SSO** tab\n\n 3. Review the values in the [SP Details](#sp-details) section\n\n 4. Follow the instructions for [setting up your own custom SAML app](https://support.google.com/a/answer/6087519) in Google Workspace Admin Help\n\n 1. The following table lists the PathcoreFlow [SP Details](#sp-details) and their equivalent fields in Google Workspace's **Service Provider Details** section:\n\n | PathcoreFlow Setting | Google Workspace Field |\n | -------------------- | ---------------------- |\n | Entity ID | Entity ID |\n | Assertion Consumer Service URL | ACS URL |\n | (unused) | Start URL |\n\n 2. Set the following Name ID settings in Google Workspace:\n - **Name ID format**: \"UNSPECIFIED\"\n - **Name ID**: \"Primary email\"\n\n 3. Configure the following in **SAML attribute mapping**:\n\n | Google Directory | App |\n | ---------------- | ---------------------- |\n | Primary email | email |\n | First name | name |\n\n 5. Enter information from Google Workspace into the fields under the [IdP Details](#idp-details) section. The following table lists the PathcoreFlow settings and their equivalent fields in Google Workspace:\n\n | PathcoreFlow Setting | Google Workspace Field |\n | -------------------- | ---------------------- |\n | Entity ID | Entity ID |\n | Single Sign On (SSO) URL | SSO URL |\n | Certificate | Certificate |\n\n 6. Complete the configuration by following the instructions in the [Configuration](#configuration) section\n\n\n\n
\n\nTo configure JumpCloud as your identity provider
\n\n 1. Click on the  **Settings** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu)\n\n 2. Click on the **SAML SSO** tab\n\n 3. Review the values in the [SP Details](#sp-details) section\n\n 4. Follow the instructions for setting up [SSO using Custom SAML Application Connectors](https://jumpcloud.com/support/sso-using-custom-saml-application-connectors) in JumpCloud Support\n\n 1. The following table lists the PathcoreFlow [SP Details](#sp-details) and their equivalent fields in JumpCloud's **SSO** section:\n\n | PathcoreFlow Setting | JumpCloud |\n | -------------------- | ---------------------- |\n | Entity ID | SP Entity ID |\n | Assertion Consumer Service URL | ACS URLs -> Add URL |\n\n 2. Set the following Name ID settings in JumpCloud:\n - **SAMLSubject NameID**: \"email\"\n - **SAMLSubject NameID Format**: \"urn:oasis:names:tc:SAML:1.1:nameid-format:emailAddress\"\n\n 3. Configure the following **User Attribute** mappings:\n\n | Service Provider Attribute Name | JumpCloud Attribute Name |\n | ------------------------------- | ------------------------ |\n | email | email |\n | name | displayname |\n\n 5. Download the certificate from JumpCloud and paste the contents of the file into the **Certificate** field under the [IdP Details](#idp-details) section\n\n 6. Enter information from JumpCloud into the fields under the [IdP Details](#idp-details) section. The following table lists the PathcoreFlow settings and their equivalent fields in JumpCloud:\n\n | PathcoreFlow Setting | JumpCloud Field |\n | -------------------- | ---------------------- |\n | Entity ID | IdP Entity ID |\n | Single Sign On (SSO) URL | IDP URL |\n\n 7. Complete the configuration by following the instructions in the [Configuration](#configuration) section\n\n\n\n
\n\nTo configure Microsoft Entra ID (formerly Azure AD) as your identity provider
\n\n 1. Click on the  **Settings** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu)\n\n 2. Click on the **SAML SSO** tab\n\n 3. Review the values in the [SP Details](#sp-details) section\n\n 4. Follow the instructions for [enabling SSO for an enterprise application](https://learn.microsoft.com/en-us/entra/identity/enterprise-apps/add-application-portal-setup-sso) in Microsoft Learn. You will need to **Create your own application**\n\n 1. The following table lists the PathcoreFlow [SP Details](#sp-details) and their equivalent fields in Microsoft Entra's **Basic SAML Configuration** section:\n\n | PathcoreFlow Setting | Microsoft Entra Field |\n | -------------------- | ---------------------- |\n | Entity ID | Identifier (Entity ID) |\n | Assertion Consumer Service URL | Reply URL (Assertion Consumer Service URL) |\n | (unused) | Sign on URL |\n | (unused) | Relay State |\n | (unused) | Logout Url |\n\n 2. Configure the following in **Attributes & Claims**:\n\n | Claim Name | Namespace | Value |\n | -------------------- | --------- | ---------------------- |\n | Unique User Identifier (Name ID) | (default) | user.userprincipalname |\n | email\\* | (leave blank) | user.userprincipalname |\n | name\\* | (leave blank) | user.displayname |\n\n \\* This will need to be added as a new claim, as the default does not allow a blank namespace.\n\n 5. Download the **Certificate (Base64)** from Microsoft Entra and paste the contents of the file in the **Certificate** field under the [IdP Details](#idp-details) section\n\n 6. Enter information from Microsoft Entra into the fields under the [IdP Details](#idp-details) section. The following table lists the PathcoreFlow settings and their equivalent fields in Microsoft Entra's **Set up <Application Name>** section:\n\n | PathcoreFlow Setting | Microsoft Entra Field |\n | -------------------- | ---------------------- |\n | Entity ID | Microsoft Entra Identifier |\n | Single Sign On (SSO) URL | Login URL |\n\n 7. Complete the configuration by following the instructions in the [Configuration](#configuration) section\n\n\n\n
\n\nTo configure Okta as your identity provider
\n\n 1. Click on the  **Settings** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu)\n\n 2. Click on the **SAML SSO** tab\n\n 3. Review the values in the [SP Details](#sp-details) section\n\n 4. Follow the instructions to [create a SAML app integration](https://help.okta.com/oie/en-us/content/topics/apps/apps_app_integration_wizard_saml.htm) in Okta Docs\n\n 1. The following table lists the PathcoreFlow [SP Details](#sp-details) and their equivalent fields in Okta's **Application Integration Wizard**:\n\n | PathcoreFlow Setting | Okta |\n | -------------------- | ---------------------- |\n | Entity ID | Audience URI (SP Entity ID) |\n | Assertion Consumer Service URL | Single sign-on URL |\n\n 2. Set the following Name ID settings in Okta:\n - **Application username**: \"Email\"\n - **Name ID format**: \"EmailAddress\"\n\n 3. Configure the following **Attribute Statements**:\n\n | Name | Value |\n | ------------------------------- | ------------------------ |\n | email | user.email |\n | name | user.firstName + \" \" + user.lastName |\n\n 5. Enter information from Okta into the fields under the [IdP Details](#idp-details) section. The following table lists the PathcoreFlow settings and their equivalent fields in Okta:\n\n | PathcoreFlow Setting | Okta Field |\n | -------------------- | ---------------------- |\n | Entity ID | Identity Provider Issuer |\n | Single Sign On (SSO) URL | Identity Provider Single Sign-On URL |\n | Certificate | X.509 Certificate |\n\n 6. Complete the configuration by following the instructions in the [Configuration](#configuration) section\n\n\n\n
\n\nTo configure OneLogin as your identity provider
\n\n 1. Click on the  **Settings** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu)\n\n 2. Click on the **SAML SSO** tab\n\n 3. Review the values in the [SP Details](#sp-details) section\n\n 4. Follow the instructions for setting up an [Advanced SAML Custom Connector](https://onelogin.service-now.com/support?id=kb_article&sys_id=8a1f3d501b392510c12a41d5ec4bcbcc&kb_category=de885d2187372d10695f0f66cebb351f) and [Configuring SSO for SAML-Enabled Applications](https://onelogin.service-now.com/support?id=kb_article&sys_id=08e6b9d9879a6990c44486e5cebb3556) in OneLogin Support\n\n 1. The following table lists the PathcoreFlow [SP Details](#sp-details) and their equivalent fields in OneLogin:\n\n | PathcoreFlow Setting | OneLogin |\n | -------------------- | ---------------------- |\n | Entity ID | Audience (EntityID) |\n | Assertion Consumer Service URL | Recipient |\n | (the regex escaped ACS URL) | ACS (Consumer) URL Validator |\n | Assertion Consumer Service URL | ACS (Consumer) URL |\n\n 2. Set the following Name ID settings in OneLogin:\n - **SAML initiator**: \"OneLogin\"\n - **SAML nameID format**: \"Email\"\n\n 3. Configure the following **Parameters**:\n\n | Service Provider Attribute Name | OneLogin Parameter Name |\n | ------------------------------- | ------------------------ |\n | email | Email |\n | name | Name |\n\n 5. Enter information from OneLogin into the fields under the [IdP Details](#idp-details) section. The following table lists the PathcoreFlow settings and their equivalent fields in OneLogin:\n\n | PathcoreFlow Setting | OneLogin Field |\n | -------------------- | ---------------------- |\n | Entity ID | Issuer URL |\n | Single Sign On (SSO) URL | SAML 2.0 Endpoint (HTTP) |\n | Certificate | X.509 Certificate |\n\n 6. Complete the configuration by following the instructions in the [Configuration](#configuration) section\n\n\n\n
\n\n\n## Configuration\n\n- **Default Permissions**: The [role](/docs/settings/roles/) to assign to users created in PathcoreFlow by [JIT Provisioning](#jit-provisioning)\n- **Default Accessible Content**: The [data group](/docs/settings/data-groups/) to assign to users created in PathcoreFlow by [JIT Provisioning](#jit-provisioning). Can be set to \"Nothing\" so that an administrator must assign accessible content to new users after they successfully log in\n- **Enable SAML Authentication**: This toggle enables the option to log in using the configured identity provider\n- **Enforce SAML SSO**: This toggle will _require_ that all users log in using the configured identity provider. Enabling this will automatically **Enable SAML Authentication**\n\nTo configure another service as your identity provider
\n\n\n The terms used by your identity provider may differ.\n
\n\n 1. Click on the  **Settings** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu)\n\n 2. Click on the **SAML SSO** tab\n\n 3. Review the values in the [SP Details](#sp-details) section\n\n 4. Follow the instructions from your identity provider to set up a new SAML application\n\n 1. The following table lists the PathcoreFlow [SP Details](#sp-details) and some common equivalent fields used by identity providers:\n\n | PathcoreFlow Setting | Alternate Names |\n | -------------------- | ---------------------- |\n | Entity ID | Audience, Identifier, Issuer, SP ID |\n | Assertion Consumer Service URL | ACS URL, Reply URL, Single Sign-On URL, SSO URL |\n\n 2. Set the following Name ID settings. Name ID may also be called SAMLSubject, Unique User ID, or App Username:\n - **Name ID**: A user's primary email address\n - **Name ID format**: \"EmailAddress\" or `urn:oasis:names:tc:SAML:1.1:nameid-format:emailAddress`\n\n 3. Configure the following SAML attribute mappings:\n\n | Name | Value |\n | ---------------- | ---------------------- |\n | email | User's email address |\n | name | User's display name or full name |\n\n 5. Enter information from your identity provider into the fields under the [IdP Details](#idp-details) section. The following table lists the PathcoreFlow settings and some common equivalent fields used by identity providers:\n\n | PathcoreFlow Setting | Alternate Names |\n | -------------------- | ---------------------- |\n | Entity ID | Identifier, Identity Provider Issuer, IdP Entity |\n | Single Sign On (SSO) URL | Login URL, SSO URL |\n | Certificate | Public key, X.509 |\n\n 6. Complete the configuration by following the instructions in the [Configuration](#configuration) section\n\n\n Users with the system-defined Administrator role can always login via their password to prevent being locked out entirely.\n
\n\n\n\n \n\n
\n\nTo finalize your SAML SSO configuration
\n\n 1. Select the desired [role](/docs/settings/roles/) from the **Default Permissions** dropdown menu\n\n 2. Select the desired [data group](/docs/settings/data-groups/) from the **Default Accessible Content** dropdown menu\n\n 3. Click on the **Verify Configuration** link to validate your configuration. This must complete successfully before you can save your changes\n\n 4. (Optional) Enable the **Enable SAML Authentication** toggle\n\n 5. (Optional) Enable the **Enforce SAML SSO** toggle if you want to require all users to use the designated identity provider to log in\n\n 6. Click on the **Save Changes** button\n\n\n\n If you have enabled Enforce SAML SSO, all users on the team must authenticate through the configured identity provider (IdP). Therefore, all users will require valid credentials for the designated provider.\n
\n\n
\n\n\n## JIT Provisioning\n\nPathcoreFlow supports just-in-time (JIT) provisioning of users by default when SAML SSO is enabled. JIT provisioning creates users in PathcoreFlow the first time they attempt to log in from their identity provider using SSO. This allows administrators to manage access to PathcoreFlow directly through their identity provider.\n\nTo disable SAML SSO for a team
\n\n 1. Click on the  **Settings** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu)\n\n 2. Click on the **SAML SSO** tab\n\n 3. Disable the **Enable SAML Authentication** toggle\n\n 4. Click on the **Save Changes** button\n\n\n A user created by JIT provisioning will be assigned the role and data group set in the Configuration section.\n
\n\n
\n","slug":"docs/settings/saml-sso"},{"frontmatter":{"title":"Storage Statistics","description":"storage statistics"},"rawBody":"---\ntitle: Storage Statistics\ndescription: storage statistics\norder: 44\nsection: Settings\n---\n\n\n# Storage Statistics\n\nFirst time JIT log in steps
\n\n 1. Log in to your identity provider. Contact your team administrator if you require assistance\n\n 2. Locate the PathcoreFlow app and launch it. The name of this app within your identity provider is configured by your team administrator and may be something different (e.g., \"Pathcore\" or \"Flow\"). You will be redirected to the PathcoreFlow login page\n\n 3. You will need to activate your account to continue. Check your email for a message which has instructions to [activate your account](/docs/settings/user-management/#account-activation). Follow those instructions. You need to set a password for PathcoreFlow, but then you will be able to log in using your identity provider credentials\n\n 4. You are now registered with the PathcoreFlow team\n\n\n\n A user only needs to activate their account once per team.\n
\n\n\n\nStorage statistics provide an overview of storage capacity and consumption as well as other statistics about the data in the Repository.\n\n\n## Statistics\n\nThe following storage information is reported\n\n- Total storage available\n- Storage used / free\n- Total data uploaded this week\n- Total data uploaded this month\n- Number of folders\n- Number of images\n- Number of snapshots created\n- Number of annotations created\n\n
\n\n
\n","slug":"docs/settings/storage-statistics"},{"frontmatter":{"title":"Team Customization","description":"team customization"},"rawBody":"---\ntitle: Team Customization\ndescription: team customization\norder: 45\nsection: Settings\n---\n\n\n# Team Customization\n\nTo view storage statistics
\n\n 1. Click on the  **Settings** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu)\n\n 2. Click on the **Storage** tab\n\n\n\nEach team has a customizable name and icon that appear at the top of the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu). The name does not appear in desktop mode while the menu is collapsed.\n\n
\n The \"Manage team\" permission flag is required to change the team name and logo.\n
\n\n\n## General\n\nAn administrator can change the team icon and name. The **Team URL** is informative only and cannot be changed on this page.\n\n\n Maximum file size for a logo is 10 MiB.\n
\n\n\n\n
\n\nTo add or replace a team icon
\n\n 1. Click on the  **Settings** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu)\n\n 2. Click on the **Team Customization** tab\n\n 3. Click on the current team icon, or the **Edit** button next to it\n\n 4. Click on **Upload Photo** and select an image from your computer\n\n 5. (Optional) Use the slider beneath the image to adjust the visible content\n\n 6. Click on the **Apply** button to save your changes, or **Cancel** to discard them\n\n\n\n
\n\nTo remove a team icon
\n\n 1. Click on the  **Settings** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu)\n\n 2. Click on the **Team Customization** tab\n\n 3. Click on the current team icon, or the **Edit** button next to it\n\n 4. Click on **Remove** to remove the icon and revert to the default\n\n\n\n \n\n
\n\n\n## Repository\n\n### Trash Retention Period\n##### [BioPharma]\n\nThe trash retention period defines how long items which have been moved to the [Trash](/docs/repository/trash/) will be retained before they are automatically deleted forever.\n\nTo change a team name
\n\n 1. Click on the  **Settings** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu)\n\n 2. Click on the **Team Customization** tab\n\n 3. Click on the **Team Name** field and type the new name into the field\n\n\n\n Changes in the Team Name field are saved automatically.\n
\n The default retention period is 30 days.\n
\n\n \n\n
\n","slug":"docs/settings/team-customization"},{"frontmatter":{"title":"Advanced Share Link Options","description":"advanced share link options"},"rawBody":"---\ntitle: Advanced Share Link Options\ndescription: advanced share link options\nsection: Share Links\norder: 26\n---\n\n\n# Advanced Share Link Options\n##### [add-on]\n\nAdvanced share link options can be used to track viewing patterns of recipients and to customize the controls that are accessible in the Viewer when the share link is accessed.\n\nTo enable advanced options, see [Image Share Links](/docs/share-links/share-link-overview/#image-share-links) and [Folder Share Links](/docs/share-links/share-link-overview/#folder-share-links).\n\nTo change the trash retention period for a team
\n\n 1. Click on the  **Settings** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu)\n\n 2. Click on the **Team Customization** tab\n\n 3. Click on the **Trash Retention Period** field\n\n 4. In the popup dialog, select from one of the preset periods, or select \"Custom\" and type in the number of days\n\n 5. Click on the **Apply** button to save your changes, or **Cancel** to discard them\n\n\n\n A ![\"Warning\"](\"../images/repository-warning-icon.svg\")
icon is shown next to the selected retention period if it is shorter than the current value, as this may cause some items in the Trash to be permanently deleted imminently.\n
icon is shown next to the selected retention period if it is shorter than the current value, as this may cause some items in the Trash to be permanently deleted imminently.\n \n The Advanced Share Links add-on is required to access these options.\n
\n\n\n## Advanced Options\n\n### View Tracking\n\nView tracking is a feature of share links and has been designed for studying the viewing habits of pathologists. When enabled for a given share link, the image regions displayed in the Viewer are logged when the image is accessed via the share link. The logged information includes a timestamp for every region displayed.\n\nView tracking can be enabled for an image share link and for a folder share link. When view tracking is enabled for a folder, viewing logs will be generated for all of the images within the folder and its subfolders, recursively, when the folder share link is used to access images.\n\nTo enable view tracking, see [Image Share Links](/docs/share-links/share-link-overview/#image-share-links) and [Folder Share Links](/docs/share-links/share-link-overview/#folder-share-links). To download logs associated with view tracking history, see [Downloading Logs](#downloading-logs).\n\n\n All access (from any user) to the image via the share link will affect the logged information.\n
\n\n\n### Collection of Annotations\n\nWhile share links are typically read-only, an exception exists for annotations. Share links can be configured to allow their recipients to create annotations. Any of the supported annotation types can be individually allowed for a given share link, to provide maximum control over the collection.\n\nAnnotations that are created via the share link will appear as shared annotations in the [Annotations Panel](/docs/viewer/annotations-panel/) for the image, are associated with the \"Anonymous\" user, and are visible by anyone that accesses the share link.\n\nTo enable collection of annotations, see [Image Share Links](/docs/share-links/share-link-overview/#image-share-links) and [Folder Share Links](/docs/share-links/share-link-overview/#folder-share-links). To download logs associated with annotations, see [Downloading Logs](#downloading-logs).\n\n\n### Hiding Viewer Tools\n\nThe set of Viewer tools that are visible in the Viewer when an image is accessed via a share link can be controlled to some extent. The following Viewer tools can be hidden: [Rotation Controls](/docs/viewer/basic-controls/#rotation-controls), [Color Management](/docs/viewer/basic-controls/#color-management), and the [Overview Tool](/docs/viewer/overview-tool/).\n\n\n## Downloading Logs\n\nSome of the advanced share link options can generate logs, including [view tracking](#view-tracking) and [collection of annotations](#collection-of-annotations). However, logs will only be generated when the view tracking has been enabled.\n\n\n\n
\n\nTo download logs of regions viewed for a share link
\n\n 1. Navigate to any folder in the Repository (click on the  **Repository** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu) then navigate to a folder)\n\n 2. Bring up the [context menu](/docs/repository/repository-operations/#context-menu) for the item\n\n 3. Click **Share**\n\n 4. In the popup dialog, click on the name of a share link with the _View Tracking Enabled_ label\n\n 5. Select the **Advanced** tab\n\n 6. Click on the  **Download Data** button underneath the **Track view history** toggle\n\n\n\n
\n\n\n### Log File Format\n\nThe log file is provided in the TSV (tab separated value) file format and is compatible with popular spreadsheet applications.\n\nEach entry in the log file has the following columns:\n\n- **Timestamp**: provides event time\n- **Source**: describes the reason the event generated the event\n- **Source ID**:\n - for Viewport events, the ID of the image\n - for Annotation events, the ID of the annotation\n- **Data**: contains the event data\n- **Data Type**: describes the type of data in the Data column\n- **Modification Method**: describes the action taken\n- **Magnification**: for Viewport events, the new magnification\n- **Image Rotation**: for Viewport events, the new rotation value (in degrees)\n- **Width**: the width of the image region on display in image coordinates @ base-level\n- **Height**: the height of the image region on display in image coordinates @ base-level\n- **Client Height**: width of the viewport in screen pixels\n- **Client Width**: height of the viewport in screen pixels\n- **Region Download Link**: a URL that provides image region overlapping with certain events and currently only supported for rect annotations (i.e., when Source is \"Annotation\" and Data Type is \"rect\")\n\n#### Source Types\n\nThe following source types are possible:\n\n- **Annotation**: produced when the annotation is created\n- **Viewport**: produced when the displayed image region changes (i.e., a pan or zoom)\n\n#### Data Types\n\nThe following Data Types are possible:\n\n- **Arrow**: Indicate the Data column contains a JSON blob that describes a series of two points produced by the arrow annotation tool\n- **Freehand**: Indicate the Data column contains a JSON blob that describes a series of points produced by the freehand annotation tool\n- **Point**: Indicate the Data column contains a JSON blob that describes a series of points produced by the bookmark annotation tool\n- **Polygon**: Indicate the Data column contains a JSON blob that describes a series of points produced by the closed polygon annotation tool\n- **Rect:** Indicate the Data column contains a JSON blob that describes a rectangle\n- **Ruler**: Indicate the Data column contains a JSON blob that describes a series of points produced by the freehand annotation tool\n\n#### Modification Methods\n\nThe following modification methods are possible:\n\n- **create**: A new annotation was created\n- **delete**: An annotation was deleted\n- **modify**: An annotation was modified\n- **move**: The displayed image region was changed\n\n### Log File Example\n\nTo download logs of regions viewed for all share links associated with an item
\n\n 1. Navigate to any folder in the Repository (click on the  **Repository** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu) then navigate to a folder)\n\n 2. Bring up the [context menu](/docs/repository/repository-operations/#context-menu) for the item\n\n 3. Click **Share**\n\n 4. In the popup dialog, click on the  button to the right of the **New Share Link** button\n\n\n\n
\n\nExample of an abbreviated log file
\n\n| Timestamp | Source | Source ID | Data | Data Type | Modification Method | Magnification | Image Rotation | Width | Height | Client Width | Client Height | Region Download Link |\n|:----------------------------- |:---------- |:---------- |:------------------------------------------------------------------------------------------------------ |:--------- |:------------------- |:------------- |:-------------- |:----- |:------ |:------------ |:------------- |:-------------------- |\n| 2022-09-21T16:09:24.951-03:00 | Viewport | 6GCMGgpoSS | `[{'x': -6900, 'y': 0}, {'x': 24900, 'y': 0}, {'x': 24900, 'y': 15847}, {'x': -6900, 'y': 15847}]` | rect | move | 1.14 | 0 | 31799 | 15847 | 1856 | 943 | |\n| 2022-09-21T16:09:35.048-03:00 | Annotation | 23 | `[{'x': 7032, 'y': 4831}]` | bookmark | create | 1.14 | 0 | | | 1856 | 943 | |\n| 2022-09-21T16:09:38.714-03:00 | Annotation | 24 | `[{'x': 8139, 'y': 6184}, {'x': 9580, 'y': 6184}, {'x': 9580, 'y': 9030}, {'x': 8139, 'y': 9030}]` | rect | create | 1.14 | 0 | 1441 | 2846 | 1856 | 943 | `https://demo.pathcore.com/api/image/6GCMGgpoSS/region?area=8139,6184,1441,2846` |\n| 2022-09-21T16:09:44.326-03:00 | Annotation | 24 | `[{'x': 7840, 'y': 9733}, {'x': 9281, 'y': 9733}, {'x': 9281, 'y': 12579}, {'x': 7840, 'y': 12579}]` | rect | modify | 1.14 | 0 | 1441 | 2846 | 1856 | 943 | `https://demo.pathcore.com/api/image/6GCMGgpoSS/region?area=7840,9733,1441,2846` |\n| 2022-09-21T16:09:50.518-03:00 | Annotation | 24 | | rect | delete | 1.14 | 0 | | | 1856 | 943 | |\n| 2022-09-21T16:09:53.885-03:00 | Viewport | 6GCMGgpoSS | `[{'x': -6900, 'y': 0}, {'x': 24900, 'y': 0}, {'x': 24900, 'y': 15847}, {'x': -6900, 'y': 15847}]` | rect | move | 1.14 | 299 | 31799 | 15847 | 1856 | 943 | |\n| 2022-09-21T16:09:58.879-03:00 | Viewport | 6GCMGgpoSS | `[{'x': -5602, 'y': 615}, {'x': 23472, 'y': 615}, {'x': 23472, 'y': 15104}, {'x': -5602, 'y': 15104}]` | rect | move | 1.25 | 299 | 29074 | 14489 | 1856 | 943 | |\n\n\n\n
\n","slug":"docs/share-links/advanced-share-link-options"},{"frontmatter":{"title":"User Management","description":"user management"},"rawBody":"---\ntitle: User Management\ndescription: user management\norder: 39\nsection: Settings\n---\n\n\n# User Management\n\nExample of an abbreviated log file in raw format
\n\n```\nTimestamp\tSource\tSource ID\tData\tData Type\tModification Method\tMagnification\tImage Rotation\tWidth\tHeight\tClient Width\tClient Height\tRegion Download Link\n2022-09-21T16:09:24.951-03:00\tViewport\t6GCMGgpoSS\t[{'x': -6900, 'y': 0}, {'x': 24900, 'y': 0}, {'x': 24900, 'y': 15847}, {'x': -6900, 'y': 15847}]\trect\tmove\t1.14\t0\t31799\t15847\t1856\t943\n2022-09-21T16:09:35.048-03:00\tAnnotation\t23\t[{'x': 7032, 'y': 4831}]\tbookmark\tcreate\t1.14\t0\t\t\t1856\t943\n2022-09-21T16:09:38.714-03:00\tAnnotation\t24\t[{'x': 8139, 'y': 6184}, {'x': 9580, 'y': 6184}, {'x': 9580, 'y': 9030}, {'x': 8139, 'y': 9030}]\trect\tcreate\t1.14\t0\t1441\t2846\t1856\t943\thttps://pathcore.com/api/image/6GCMGgpoSS/region?area=8139,6184,1441,2846\n2022-09-21T16:09:44.326-03:00\tAnnotation\t24\t[{'x': 7840, 'y': 9733}, {'x': 9281, 'y': 9733}, {'x': 9281, 'y': 12579}, {'x': 7840, 'y': 12579}]\trect\tmodify\t1.14\t0\t1441\t2846\t1856\t943\thttps://pathcore.com/api/image/6GCMGgpoSS/region?area=7840,9733,1441,2846\n2022-09-21T16:09:50.518-03:00\tAnnotation\t24\t\trect\tdelete\t1.14\t0\t\t\t1856\t943\n2022-09-21T16:09:53.885-03:00\tViewport\t6GCMGgpoSS\t[{'x': -6900, 'y': 0}, {'x': 24900, 'y': 0}, {'x': 24900, 'y': 15847}, {'x': -6900, 'y': 15847}]\trect\tmove\t1.14\t299\t31799\t15847\t1856\t943\n2022-09-21T16:09:58.879-03:00\tViewport\t6GCMGgpoSS\t[{'x': -5602, 'y': 615}, {'x': 23472, 'y': 615}, {'x': 23472, 'y': 15104}, {'x': -5602, 'y': 15104}]\trect\tmove\t1.25\t299\t29074\t14489\t1856\t943\n```\n\n\n\nThe user management capabilities allow administrators to create new users and manage attributes of existing user accounts.\n\n
\n The \"Manage users\" permission flag is required to see the list of users.\n
\n\n\n## User Accounts\n\nEach user account in the system has the following attributes:\n\n- A name\n- An email address\n- A role - the actions users can perform with the content they can access\n- Accessible content - the data accessible to a user\n- Account status (e.g., active, disabled, awaiting activation)\n- Account creation time\n\nThe account name and email address are defined by an administrator when the account is created. Beyond this point, only the user can change these properties (e.g., name, password, picture, and signature) from the user’s [My Account](/docs/settings/my-account/).\n\n\n\n
\n\nTo view the list of accounts currently registered, and their properties
\n\n 1. Click on the  **Settings** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu)\n\n 2. Click on the **Users** tab\n\n\n\n
\n\nTo sort the user account list
\n\n 1. Click on the  **Settings** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu)\n\n 2. Click on the **Users** tab\n\n 3. From the table header, click on a column until the desired sort order is shown (sort order is shown with  for ascending order and  for descending order in the table header adjacent to the selected column)\n\n\n\n
\n\nTo search for an existing user account by name or email address
\n\n 1. Click on the  **Settings** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu)\n\n 2. Click on the **Users** tab\n\n 3. Type a few characters in the search bar above the user table\n\n\n\n
\n\n\n## Creating User Accounts\n\n### Account Creation\n\nBefore creating users, it is recommended to have an understanding of [Permissions](/docs/settings/permissions/) and [Accessible Content](/docs/settings/accessible-content/). To streamline user creation, please review the existing [Roles](/docs/settings/roles/) and [Data Groups](/docs/settings/data-groups/) to ensure you are familiar with the available options and if necessary, create new roles and data groups to suit the needs of new users.\n\nNewly created accounts will be marked as \"awaiting activation\" and the new user will not be able to log in until [Account Activation](#account-activation) is completed.\n\nTo show/hide accounts that are not active
\n\n 1. Click on the  **Settings** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu)\n\n 2. Click on the **Users** tab\n\n 3. Click on the  **Filter** button\n\n 4. Enable the **Show disabled users** toggle to include in the listing users which have been disabled by an administrator\n\n 5. Enable the **Show non-activated users** toggle to include in the listing users who have not yet completed the activation process\n\n\n Newly created users cannot access any data by default, unless a Data Group and/or Role is selected during user creation.\n
\n\n\n\n
\n\n\n### Account Activation\n\nAfter a user account has been created by a team administrator, the system will automatically send an account activation notification to the new user by email. Once received, the user may click on the **Activate** button from their email to choose a password, review the terms and conditions and complete other activation steps as may be required.\n\nTo create a user account
\n\n 1. Click on the  **Settings** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu)\n\n 2. Click on the **Users** tab\n\n 3. Click on the **Create User** button\n\n 4. Enter the user’s name in the **Name** field\n\n 5. Enter the user’s email address in the **Email** field\n\n 6. (Optional) Choose one of the following options for the user’s permissions:\n 1. Select an option from the **Role** dropdown menu; or\n 2. Click on the **Customize Permissions** button and select individual [Permission Flags](/docs/settings/permissions/#permission-flags)\n\n 7. (Optional) Choose one of the following options for the user’s accessible content:\n 1. Select an option from the **Data Group** dropdown menu; or\n 2. To allow access to all data: click on the **Customize Accessible Content** button and enable the **Grant access to all team content** toggle at the top of the Accessible Content popup dialog; or\n 3. To limit the access to a set of folders: click on the **Customize Accessible Content** button and select the folders that should be accessible to the user\n\n 8. Click on the **Create User** button to finish\n\n\n Activation emails are incorrectly marked as spam by some email services. Be sure to check your spam filter.\n
\n\n\n### Resending Activation Notification\n\nIf the user is having difficulty finding an activation email, even after checking their spam folder, or for any other reason, the notification can be resent by the team administrator.\n\n\n\n
\n\n\n## Modifying User Accounts\n\nAn administrator can modify permissions of users, their accessible content and account status. However, names associated with accounts can only be changed by the user via [My Account](/docs/settings/my-account/).\n\nTo resend a user account activation notification
\n\n 1. Click on the  **Settings** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu)\n\n 2. Click on the **Users** tab\n\n 3. Locate the user in the users table and click on the **More** menu on the right-hand side of the row\n\n 4. Select the **Resend Activation Link** option in the popup menu\n\n\n The \"Manage users\" permission flag is required to modify user accounts.\n
\n\n\n### Modifying Permissions\n\n[Permissions](/docs/settings/permissions/) define the set of actions that users can perform with the data they can access (e.g., download, edit, view). While the permissions assigned to each user can be customized, it may be more convenient to create a common [Role](/docs/settings/roles/) to express the permissions for user types (e.g., viewer, editor, administrator).\n\n\n\n
\n\n\n### Modifying Accessible Content\n\n[Accessible Content](/docs/settings/accessible-content/) defines the set of folders that can be accessed by users. While accessible content can be customized for each user, it may be convenient to create a common [Data Group](/docs/settings/data-groups/) for users that require access to the same folders (e.g., staff in a department or team). A Data Group can be associated with multiple users.\n\nTo modify the permission/role associated with a user’s account
\n\n 1. Click on the  **Settings** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu)\n\n 2. Click on the **Users** tab\n\n 3. Locate the user in the users table and click on the **More** menu on the right-hand side of the row\n\n 4. Select the **Edit Role/Permissions** option in the popup menu\n\n 5. Choose one of the following options:\n 1. Select an option from the **Role** dropdown menu; or\n 2. Click on the **Customize Permissions** button and select individual [Permission Flags](/docs/settings/permissions/#permission-flags)\n\n 6. Click on the **Save** button\n\n\n\n
\n\n\n### Invalidate User’s Session(s)\n\nBy default, users are not required to re-authenticate until they have logged out or until the application cookies have been cleared. However, an administrator can force a user to re-authenticate by invalidating their sessions.\n\nTo modify the accessible content or the data group associated with user accounts
\n\n 1. Click on the  **Settings** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu)\n\n 2. Click on the **Users** tab\n\n 3. Locate the user in the users table and click on the **More** menu on the right-hand side of the row\n\n 4. Select the **Edit Accessible Content** option in the popup menu\n\n 5. Choose one of the following options:\n 1. Select an option from the **Data Group** dropdown menu; or\n 2. To allow access to all data: enable the **Grant access to all team content** toggle at the top of the Accessible Content popup dialog; or\n 3. To limit the access to a set of folders: select the folders that should be accessible to the user\n\n 6. Click on the **Save** button\n\n\n\n
\n\n\n### Disable User Accounts\n\nIf an account is no longer required it can be disabled. At this time, there is no way to delete user accounts, since these may be connected to [activity logs](/docs/repository/activity-logs/) that are collected during normal application use. It’s important to note that the application does not collect personal information other than a user’s name and email address. In order to meet any regulatory requirements with respect to user privacy, please contact our support team.\n\nTo invalidate a user’s session
\n\n 1. Click on the  **Settings** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu)\n\n 2. Click on the **Users** tab\n\n 3. Locate the user in the users table and click on the **More** menu on the right-hand side of the row\n\n 4. Select the **Invalidate Sessions** option in the popup menu\n\n\n\n
\n","slug":"docs/settings/user-management"},{"frontmatter":{"title":"Embedding an Image","description":"embedding an image"},"rawBody":"---\ntitle: Embedding an Image\ndescription: embedding an image\nsection: Share Links\norder: 25\n---\n\n\n# Embedding an Image\n\nTo disable a user account or to enable a previously disabled account
\n\n 1. Click on the  **Settings** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu)\n\n 2. Click on the **Users** tab\n\n 3. Locate the user in the users table and click on the **More** menu on the right-hand side of the row\n\n 4. Select the **Disable Account** or **Enable Account** option in the popup menu as appropriate\n\n 5. Click on **Yes** to confirm\n\n\n\nThe embed feature of share links may be used to create interactive experiences with images on your own web pages or to simply show notable images and annotations. To embed an image into a webpage, copy the HTML snippet provided in the share link properties dialog into your own website. Image embedding uses the HTML
\n Embedded images may not work in browsers that restrict third-party cookies.\n
\n\n\n\n
\n Images embedded in local HTML files do not work in Apple Safari. This limitation does not apply to webpages served over a network.\n
\n\n\n\n
\n\nTo retrieve the embed code for an image from the Repository
\n\n 1. Navigate to any folder in the Repository (click on the  **Repository** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu) then navigate to a folder)\n\n 2. Bring up the [context menu](/docs/repository/repository-operations/#context-menu) for the image\n\n 3. Click **Share**\n\n 4. In the popup dialog, click on the name of the share link or click on the **New Share Link** button to create a new one\n\n 5. Click on the **Embed Image** tab\n\n 6. (Optional) Configure the embedded image settings\n 1. (Optional) Set the **Width** (may include units such as % and px)\n 2. (Optional) Set the **Height** (may include units such as % and px)\n\n 7. Click on the  button to the right of the HTML snippet to copy it to the clipboard\n\n 8. Paste the HTML snippet into your webpage\n\n\n\n
\n","slug":"docs/share-links/embedding-an-image"},{"frontmatter":{"title":"","description":null},"rawBody":"---\nredirect: /docs/share-links/share-link-overview/\n---\n","slug":"docs/share-links/"},{"frontmatter":{"title":"Share Link Overview","description":"share link overview"},"rawBody":"---\ntitle: Share Link Overview\ndescription: share link overview\nsection: Share Links\norder: 23\n---\n\n\n# Share Link Overview\n\nTo retrieve the embed code for an image from within the Viewer
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. Click on the name of the share link or click on the **New Share Link** button to create a new one\n\n 4. Click on the **Embed Image** tab\n\n 5. (Optional) Configure the embedded image settings\n 1. (Optional) Set the **Width** (may include units such as % and px)\n 2. (Optional) Set the **Height** (may include units such as % and px)\n 3. (Optional) Enable the **Start at current location** toggle to use the current view as the initial view for the embedded image\n\n 6. Click on the  button to the right of the HTML snippet to copy it to the clipboard\n\n 7. Paste the HTML snippet into your webpage\n\n\n\nHave files or folders you would like to share? You can generate a unique and, optionally, time-limited share link for an image or a folder. Share links provide read-only access (unless [Collection of Annotations](/docs/share-links/advanced-share-link-options/#collection-of-annotations) is enabled) to the item(s) being shared and their children, but do not require the recipient to authenticate (i.e., can be accessed without logging in). Share links can be used by anyone that knows the share link URL, without an account.\n\n
\n Anyone with access to the share link URL will be able to view the content associated with the share link. It’s recommended to use share links only with trusted collaborators or for public data sharing.\n
\n\n\n## Image Share Links\n\nAn image share link provides read-only access (unless [Collection of Annotations](/docs/share-links/advanced-share-link-options/#collection-of-annotations) is enabled) to a single image and its metadata such as shared annotations, Custom Fields, and analysis results. Image share links can be created from the Repository page or from within the Viewer.\n\nShare links created from within the Viewer provide additional flexibility — primarily the ability to control the recipient's initial view. See [Link to Current Location](#link-to-current-location) for more details.\n\n\n\n
\n\nTo create an image share link from the Repository
\n\n 1. Navigate to any folder in the Repository (click on the  **Repository** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu) then navigate to a folder)\n\n 2. Bring up the [context menu](/docs/repository/repository-operations/#context-menu) for the image\n\n 3. Click **Share**\n\n 4. Click on the **New Share Link** button\n\n 5. (Optional) Configure the link. See [Share Link Properties](#share-link-properties) for more details\n 1. (Optional) Document the purpose of the link in the **Name** field\n 2. (Optional) Choose an expiry date by clicking on the **Expires** field, or choose a preset lifetime from below the field\n 3. (Optional) Enable the **Anonymize data** toggle. See [Anonymize Data](#anonymize-data) for more details\n 4. (Optional) Enable the **Show annotations** toggle to make shared annotations visible via the share link\n\n 6. (Optional) Select the **Advanced** tab to configure [advanced share link options](/docs/share-links/advanced-share-link-options/)\n 1. (Optional) Enable **Track view history**. See [View Tracking](/docs/share-links/advanced-share-link-options/#view-tracking) for more details\n 2. (Optional) In the **Customize viewer** section, you may configure the Viewer by [hiding certain tools](/docs/share-links/advanced-share-link-options/#hiding-viewer-tools)\n 3. (Optional) In the **Allow annotations** section, you may enable the [collection of annotations](/docs/share-links/advanced-share-link-options/#collection-of-annotations) by selecting tools that will be enabled for the share link\n\n 7. (Optional) In the **Link** tab, click on the  button to the right of the link field to copy the URL\n\n 8. (Optional) Email the share link to the intended recipients\n 1. Add one or more email addresses to the **Email this link** section\n 2. (Optional) Add a message for the recipients to the **Message** section\n 3. Click on the **Send Email** button\n\n 9. Click on the **X** button at the top right of the popup dialog or anywhere outside of the dialog box to close it\n\n\n\n All changes are saved automatically.\n
\n\n\n\n
\n\n\n## Folder Share Links\n\nA folder share link provides read-only access (unless [Collection of Annotations](/docs/share-links/advanced-share-link-options/#collection-of-annotations) is enabled) to the contents of a folder and its subfolders recursively, including all the metadata associated with these items. A folder share link can be used to navigate the folder and its children, including any images that are contained within them. Folder share links are ideal for sharing an entire dataset, case or study.\n\nTo create an image share link from within the Viewer
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. Click on the **New Share Link** button\n\n 4. (Optional) Configure the link. See [Share Link Properties](#share-link-properties) for more details\n 1. (Optional) Document the purpose of the link in the **Name** field\n 2. (Optional) Choose an expiry date by clicking on the **Expires** field, or choose a preset lifetime from below the field\n 3. (Optional) Enable the **Link to current location** toggle to set the ROI when the link is first opened to match the current position in the Viewer\n 4. (Optional) Enable the **Anonymize data** toggle. See [Anonymize Data](#anonymize-data) for more details\n 5. (Optional) Enable the **Show annotations** toggle to make shared annotations visible via the share link\n\n 5. (Optional) Select the **Advanced** tab to configure [advanced share link options](/docs/share-links/advanced-share-link-options/)\n 1. (Optional) Enable **Track view history**. See [View Tracking](/docs/share-links/advanced-share-link-options/#view-tracking) for more details\n 2. (Optional) In the **Customize viewer** section, you may configure the Viewer by [hiding certain tools](/docs/share-links/advanced-share-link-options/#hiding-viewer-tools)\n 3. (Optional) In the **Allow annotations** section, you may enable the [collection of annotations](/docs/share-links/advanced-share-link-options/#collection-of-annotations) by selecting tools that will be enabled for the share link\n\n 6. (Optional) In the **Link** tab, click on the  button to the right of the link field to copy the URL\n\n 7. (Optional) Email the share link to the intended recipients\n 1. Add one or more email addresses to the **Email this link** section\n 2. (Optional) Add a message for the recipients to the **Message** section\n 3. Click on the **Send Email** button\n\n 8. Click on the **X** button at the top right of the popup dialog or anywhere outside of the dialog box to close it\n\n\n\n All changes are saved automatically.\n
\n\n\n\n
\n\nTo create a share link for the current folder
\n\n 1. Navigate to any folder in the Repository (click on the  **Repository** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu) then navigate to a folder)\n\n 2. Click on the  button next to the current folder's breadcrumb\n\n 3. Click **Share**\n\n 4. Click on the **New Share Link** button\n\n 5. (Optional) Configure the link. See [Share Link Properties](#share-link-properties) for more details\n 1. (Optional) Document the purpose of the link in the **Name** field\n 2. (Optional) Choose an expiry date by clicking on the **Expires** field, or choose a preset lifetime from below the field\n 3. (Optional) Enable the **Anonymize data** toggle. See [Anonymize Data](#anonymize-data) for more details\n 4. (Optional) Enable the **Show annotations** toggle to make shared annotations visible via the share link\n\n 6. (Optional) Select the **Advanced** tab to configure [advanced share link options](/docs/share-links/advanced-share-link-options/)\n 1. (Optional) Enable **Track view history**. See [View Tracking](/docs/share-links/advanced-share-link-options/#view-tracking) for more details\n 2. (Optional) In the **Customize viewer** section, you may configure the Viewer by [hiding certain tools](/docs/share-links/advanced-share-link-options/#hiding-viewer-tools)\n 3. (Optional) In the **Allow annotations** section, you may enable the [collection of annotations](/docs/share-links/advanced-share-link-options/#collection-of-annotations) by selecting tools that will be enabled for the share link\n\n 7. (Optional) In the **Link** tab, click on the  button to the right of the link field to copy the URL\n\n 8. (Optional) Email the share link to the intended recipients\n 1. Add one or more email addresses to the **Email this link** section\n 2. (Optional) Add a message for the recipients to the **Message** section\n 3. Click on the **Send Email** button\n\n 9. Click on the **X** button at the top right of the popup dialog or anywhere outside of the dialog box to close it\n\n\n\n All changes are saved automatically.\n
\n\n\n\n
\n\n\n## Attachment Share Links\n\nAn attachment share link provides read-only access to any file in the Repository other than an image. Share links for attachments do not have advanced options.\n\nTo create a share link for a folder
\n\n 1. Navigate to any folder in the Repository (click on the  **Repository** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu) then navigate to a folder)\n\n 2. Bring up the [context menu](/docs/repository/repository-operations/#context-menu) for the folder\n\n 3. Click **Share**\n\n 4. Click on the **New Share Link** button\n\n 5. (Optional) Configure the link. See [Share Link Properties](#share-link-properties) for more details\n 1. (Optional) Document the purpose of the link in the **Name** field\n 2. (Optional) Choose an expiry date by clicking on the **Expires** field, or choose a preset lifetime from below the field\n 3. (Optional) Enable the **Anonymize data** toggle. See [Anonymize Data](#anonymize-data) for more details\n 4. (Optional) Enable the **Show annotations** toggle to make shared annotations visible via the share link\n\n 6. (Optional) Select the **Advanced** tab to configure [advanced share link options](/docs/share-links/advanced-share-link-options/)\n 1. (Optional) Enable **Track view history**. See [View Tracking](/docs/share-links/advanced-share-link-options/#view-tracking) for more details\n 2. (Optional) In the **Customize viewer** section, you may configure the Viewer by [hiding certain tools](/docs/share-links/advanced-share-link-options/#hiding-viewer-tools)\n 3. (Optional) In the **Allow annotations** section, you may enable the [collection of annotations](/docs/share-links/advanced-share-link-options/#collection-of-annotations) by selecting tools that will be enabled for the share link\n\n 7. (Optional) In the **Link** tab, click on the  button to the right of the link field to copy the URL\n\n 8. (Optional) Email the share link to the intended recipients\n 1. Add one or more email addresses to the **Email this link** section\n 2. (Optional) Add a message for the recipients to the **Message** section\n 3. Click on the **Send Email** button\n\n 9. Click on the **X** button at the top right of the popup dialog or anywhere outside of the dialog box to close it\n\n\n\n All changes are saved automatically.\n
\n\n\n\n
\n\n\n## Share Link Properties\n\nShare links have a number of properties that make it easier to share exactly the content that is required.\n\n\n### Name\n\nShare link names can be used to distinguish different links and/or to summarize the reason for which they were created. The name is not visible to recipients of the share link.\n\n\n### Expiry Date\n\nAn expiry date may be set to limit the duration of time that share links can be accessed by recipients. Without an expiry date, recipients can access data until the links are deleted.\n\nEmbedded images inherit the expiry date of a share link, if set. After a share link has expired, the related embedded images will no longer work.\n\n\n### Anonymize Data\n\nShare links can be anonymized by enabling the **Anonymize data** toggle. With this option selected the following restrictions are applied to the share link:\n\n- Custom Fields values that have been marked as having PI are hidden, see [Custom Fields Settings](/docs/metadata/custom-fields/#custom-field-settings) for details\n- Slide labels associated with WSI, other than burned-in annotations, are hidden\n- Recipients will not be able to download images\n\nEmbedded images inherit the anonymization property of a share link.\n\nTo create a share link for an attachment
\n\n 1. Navigate to any folder in the Repository (click on the  **Repository** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu) then navigate to a folder)\n\n 2. Bring up the [context menu](/docs/repository/repository-operations/#context-menu) for the item\n\n 3. Click **Share**\n\n 4. Click on the **New Share Link** button\n\n 5. (Optional) Configure the link. See [Share Link Properties](#share-link-properties) for more details\n 1. (Optional) Document the purpose of the link in the **Name** field\n 2. (Optional) Choose an expiry date by clicking on the **Expires** field, or choose a preset lifetime from below the field\n\n 6. (Optional) In the **Link** tab, click on the  button to the right of the link field to copy the URL\n\n 7. (Optional) Email the share link to the intended recipients\n 1. Add one or more email addresses to the **Email this link** section\n 2. (Optional) Add a message for the recipients to the **Message** section\n 3. Click on the **Send Email** button\n\n 8. Click on the **X** button at the top right of the popup dialog or anywhere outside of the dialog box to close it\n\n\n\n All changes are saved automatically.\n
\n\n\n If the user creating a share link lacks the \"View Protected Information\" permission flag, then the Anonymize data toggle defaults to enabled and cannot be disabled.\n
\n\n
\n The option to anonymize data only applies to share links for images and folders. Share links to attachments do not have this toggle.\n
\n\n\n### Show Annotations\n\nTo make the annotations of an image visible to share link recipients, enable the **Show annotations** toggle. With this toggle selected, all shared annotations will be visible to recipients but your private annotations remain hidden.\n\nEmbedded images inherit this property from share links. When enabled, annotations on the image will be visible via an embedded image.\n\n\n### Link to Current Location\n\nThe **Link to current location** toggle, when enabled, configures the share link to replicate the current scene in the Viewer, at the moment the share link is generated, when the link is first accessed. This option is only available if a share link is created from within the Viewer. The scene is defined by the point at the center of the viewport and current magnification.\n\nEmbedded images inherit this property from share links. When enabled, the code snippet in the embedded image tab will be configured to show the current scene as the default view.\n","slug":"docs/share-links/share-link-overview"},{"frontmatter":{"title":"Managing Share Links","description":"managing share links"},"rawBody":"---\ntitle: Managing Share Links\ndescription: managing share links\nsection: Share Links\norder: 24\n---\n\n\n# Managing Share Links\n\n\n\nShare links can be viewed, edited and deleted after they have been created. In order to see the share links that have been generated for an item, bring up the [context menu](/docs/repository/repository-operations/#context-menu) for the item in the Repository and select **Share**. At present, there is no way to see all the shared links that have been generated by all users and for all images and folders.\n\n
\n If there are any share links associated with an item, a share icon is displayed to the right of its name in the Repository listing. Hovering over the icon shows how many share links are associated with the item.\n
\n\n\n\n
\n\nTo edit a share link for the current folder from the Repository
\n\n 1. Navigate to any folder in the Repository (click on the  **Repository** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu) then navigate to a folder)\n\n 2. Click on the  button next to the current folder's breadcrumb. This icon only appears if at least one share link has been created for the current folder\n\n 3. In the popup dialog, click on the name of the share link to edit\n\n 4. (Optional) Configure the link. See [Share Link Properties](/docs/share-links/share-link-overview/#share-link-properties) for more details\n 1. (Optional) Document the purpose of the link in the **Name** field\n 2. (Optional) Choose an expiry date by clicking on the **Expires** field, or choose a preset lifetime from below the field\n 3. (Optional) Enable the **Anonymize data** toggle. See [Anonymize Data](/docs/share-links/share-link-overview/#anonymize-data) for more details\n 4. (Optional) Enable the **Show annotations** toggle to make shared annotations visible via the share link\n\n 5. (Optional) In the **Link** tab, click on the  button to the right of the link field to copy the URL\n\n 6. (Optional) Email the share link to the intended recipients\n 1. Add one or more email addresses to the **Email this link** section\n 2. (Optional) Add a message for the recipients to the **Message** section\n 3. Click on the **Send Email** button\n\n 7. Click on the **X** button at the top right of the popup dialog or anywhere outside of the dialog box to close it\n\n\n\n All changes are saved automatically.\n
\n\n\n\n
\n\nTo delete a share link for the current folder from the Repository
\n\n 1. Navigate to any folder in the Repository (click on the  **Repository** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu) then navigate to a folder)\n\n 2. Click on the  button next to the current folder's breadcrumb. This icon only appears if at least one share link has been created for the current folder\n\n 3. In the popup dialog, click on the  button adjacent to the share link\n\n 4. Click on the **Delete Link** button to confirm if you are sure you wish to remove the item. To cancel the delete action, click on the **Cancel** button or press the **Escape** key\n\n\n\n
\n\nTo edit a share link for any item from the Repository
\n\n 1. Navigate to any folder in the Repository (click on the  **Repository** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu) then navigate to a folder)\n\n 2. Bring up the [context menu](/docs/repository/repository-operations/#context-menu) for the item\n\n 3. Click **Share**\n\n 4. In the popup dialog, click on the name of the share link to edit\n\n 5. (Optional) Configure the link. See [Share Link Properties](/docs/share-links/share-link-overview/#share-link-properties) for more details\n 1. (Optional) Document the purpose of the link in the **Name** field\n 2. (Optional) Choose an expiry date by clicking on the **Expires** field, or choose a preset lifetime from below the field\n 3. (Optional) Enable the **Anonymize data** toggle. See [Anonymize Data](/docs/share-links/share-link-overview/#anonymize-data) for more details\n 4. (Optional) Enable the **Show annotations** toggle to make shared annotations visible via the share link\n\n 6. (Optional) In the **Link** tab, click on the  button to the right of the link field to copy the URL\n\n 7. (Optional) Email the share link to the intended recipients\n 1. Add one or more email addresses to the **Email this link** section\n 2. (Optional) Add a message for the recipients to the **Message** section\n 3. Click on the **Send Email** button\n\n 8. Click on the **X** button at the top right of the popup dialog or anywhere outside of the dialog box to close it\n\n\n\n All changes are saved automatically.\n
\n\n\n\n
\n\nTo delete a share link for any item from the Repository
\n\n 1. Navigate to any folder in the Repository (click on the  **Repository** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu) then navigate to a folder)\n\n 2. Bring up the [context menu](/docs/repository/repository-operations/#context-menu) for the item\n\n 3. Click **Share**\n\n 4. In the popup dialog, click on the  button adjacent to the share link\n\n 5. Click on the **Delete Link** button to confirm if you are sure you wish to remove the item. To cancel the delete action, click on the **Cancel** button or press the **Escape** key\n\n\n\n
\n\nTo edit a share link for an image from within the Viewer
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. Click on the name of the share link to edit\n\n 4. (Optional) Configure the link. See [Share Link Properties](/docs/share-links/share-link-overview/#share-link-properties) for more details\n 1. (Optional) Document the purpose of the link in the **Name** field\n 2. (Optional) Choose an expiry date by clicking on the **Expires** field, or choose a preset lifetime from below the field\n 3. (Optional) Enable the **Link to current location** toggle to set the ROI when the link is first opened to match the current position in the Viewer\n 4. (Optional) Enable the **Anonymize data** toggle. See [Anonymize Data](/docs/share-links/share-link-overview/#anonymize-data) for more details\n 5. (Optional) Enable the **Show annotations** toggle to make shared annotations visible via the share link\n\n 5. (Optional) In the **Link** tab, click on the  button to the right of the link field to copy the URL\n\n 6. (Optional) Email the share link to the intended recipients\n 1. Add one or more email addresses to the **Email this link** section\n 2. (Optional) Add a message for the recipients to the **Message** section\n 3. Click on the **Send Email** button\n\n 7. Click on the **X** button at the top right of the popup dialog or anywhere outside of the dialog box to close it\n\n\n\n All changes are saved automatically.\n
\n\n\n\n
\n","slug":"docs/share-links/managing-share-links"},{"frontmatter":{"title":"Basic Controls","description":"basic controls"},"rawBody":"---\ntitle: Basic Controls\ndescription: basic controls\nsection: Viewer\norder: 15\n---\n\n\n# Basic Controls\n\nTo delete a share link for an image from within the Viewer
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. In the popup dialog, click on the  button adjacent to the share link\n\n 4. Click on the **Delete Link** button to confirm if you are sure you wish to remove the item. To cancel the delete action, click on the **Cancel** button or press the **Escape** key\n\n\n\n\n## Panning\n\nThe Viewer supports multiple ways for navigating images in the Viewer using the mouse and keyboard.\n\n
\n\n
\n\nTo pan an image with the mouse from within the Viewer
\n\n 1. Press and hold the left mouse button anywhere on the image\n\n 2. Drag with the mouse to navigate the image\n\n\n\n
\n\nTo pan an image with the keyboard from within the Viewer
\n\n 1. Click anywhere on the image (to set focus)\n\n 2. Use the arrow keys (up, down, left, right) to navigate the image\n\n\n\n
\n\n\n## Magnification\n\nMagnification controls are automatically provided for images that define an objective magnification and for images that are heuristically determined to be whole slide images (e.g., a TIFF file containing a description from a known WSI scanner manufacturer that also has a well-defined pixel size).\n\nThe Viewer will provide preset magnification buttons that are appropriate for the current image, if this information is provided by the image or can be determined heuristically. The preset buttons are accessible from the bottom left side of the image viewport, above the current magnification. For any image where magnification cannot be determined, the magnification controls are replaced with scaling controls (e.g., 50%, 100%).\n\nTo show the current position of the cursor
\n\n 1. Click on the  button in the Viewer top bar\n\n 2. Hover over the image to display a tooltip with the cursor's x and y position. It also includes the red (R), green (G), and blue (B) values for brightfield images\n\n 3. (Optional) Click on the  button to turn off the tooltip.\n\n\n The current magnification is displayed in the Viewer top bar and at the bottom left corner of each image\n
\n\n\n\n
\n\nTo change magnification (or scale factor) using the mouse from within the Viewer
\n\n 1. Click anywhere on the image (to set focus)\n\n 2. Use the wheel on the mouse to change magnification fluidly\n\n\n\n
\n\n\n### Heuristically Determined Magnification\n\nImage pixel size is loosely related to the scanned magnification. WSI scanner manufacturers typically define a conversion between pixel size and magnification. Where magnification is not explicitly defined in an image, the pixel size will be used to infer the equivalent objective magnification of the image. In many cases, scanned magnification of 20x is approximately equal to 0.5μm per pixel.\n\n\n### Digital Zoom\n\nYou can zoom an image beyond its native resolution up to 400%. For example, if an image has a maximum magnification of 20x, it can be scaled up to 80x.\n\nThe current magnification is always visible in the bottom left corner of an image. When digital zoom is enabled for an image, the current magnification is shown with a blue border and an adjacent \"Digital Zoom\" indicator.\n\n\n## Focal Planes\n\nFocal planes are automatically detected when present in supported images. If the image has multiple [sub-images](/docs/viewer/overview/#sub-images), the focal plane for each sub-image can be independently configured by selecting the appropriate sub-image from the dropdown menu.\n\nThe focal plane controls are visible in the bottom left bottom of the image viewport only when focal planes are detected in an image.\n\nTo change magnification using the keyboard from within the Viewer
\n\n 1. Click anywhere on the image (to set focus)\n\n 2. Use the +/- buttons to change magnification in small increments\n\n\n\n
\n\nTo see available focal planes for an image
\n\n 1. Click on the current focal plane indicator\\* to reveal the focal plane dialog\n\n 2. Click into the Focal Plane dropdown menu to view available planes\n\n 3. Click on the **x** button to close the focal plane dialog\n\n\n \\* The focal plane controls consist of  and  arrows and a numeric indicator displaying the current focal plane offset (e.g., \"0 μm\"). If available for the current image, these controls are located on the bottom left-hand side of the image viewport immediately above the magnification controls.\n\n\n\n
\n\nTo change the focal plane using the mouse
\n\n 1. Click on the  or  buttons on the focal plane controls\\*\n\n\n \\* The focal plane controls consist of  and  arrows and a numeric indicator displaying the current focal plane offset (e.g., \"0 μm\"). If available for the current image, these controls are located on the bottom left-hand side of the image viewport immediately above the magnification controls.\n\n\n\n
\n\n\n## Rotation Controls\n\nThe rotation tool is located on the bottom left corner of the image viewport. The rotation value is always saved for each user and will be preserved the next time you view the image.\n\nTo change the focal plane using the mouse wheel
\n\n 1. Click on the image\n\n 2. Hold down the **Shift** key on the keyboard and simultaneously use the mouse wheel to fly through the available focal planes\n\n\n\n
\n\nTo enable the rotation tool
\n\n 1. Hover or click on the image to reveal the toolbar at the top left of the panel\n\n 2. Click on the  button to expand the toolbar if necessary\n\n 3. Click on the  button in the toolbar to show or hide the rotation tool\n\n\n\n
\n\nTo rotate using the mouse
\n\n 1. Click and drag the ball around the outside of the rotation tool to the desired value\n\n 2. Click in the middle of the rotation tool (where the rotation value is displayed) and type a value between (-360) to +360 degrees\n\n 3. To reset rotation to 0°, click in the middle of the rotation tool and type 0\n\n\n\n The rotation tool accepts values with a precision of 0.1.\n
\n\n\n\n
\n\n\n## Color Management\n\nThe color management tools can be used to apply an ICC color profile within the Viewer. The application of ICC profiles ensures a high degree of color reproducibility across different monitors and can be used to overcome/reduce color variability across multiple devices.\n\nTo rotate using the keyboard
\n\n 1. Hold the **Alt** key and press the **up arrow** or **down arrow** key to rotate by 1° clockwise or counter-clockwise, respectively\n\n 2. Hold the **Alt** key and press the **PageUp** or **PageDown** key to rotate by 10° clockwise or counter-clockwise, respectively\n\n\n Color Management is available for RGB images and disabled by default; users can choose their preference.\n
\n\n\n\n
\n\n\n## Full Screen Mode\n\nTo enlarge the image viewport, so that it fills your screen, click on the  button in the Viewer top bar. When done, press the **Escape** key on your keyboard to exit full screen mode.\n\n\n## Keyboard Shortcuts\n\nThe following keyboard shortcuts are available when using the keyboard:\n\n| Shortcut | Action |\n| -------- | ------ |\n| A | Draw an arrow annotation |\n| B | Draw a bookmark annotation |\n| C | Draw an ellipse annotation |\n| P | Draw a polygon annotation |\n| F | Draw a freehand annotation |\n| R | Draw a rectangle annotation |\n| U | Draw a ruler annotation |\n| S | Create a snapshot |\n| Alt + ↑ | Rotate clockwise 1° |\n| Alt + ↓ | Rotate counter-clockwise 1° |\n| Alt + PageUp | Rotate clockwise 10° |\n| Alt + PageDown | Rotate counter-clockwise 10° |\n| Ctrl + → | Next Image |\n| Ctrl + ← | Previous Image |\n","slug":"docs/viewer/basic-controls"},{"frontmatter":{"title":"Figure Maker","description":"figure maker"},"rawBody":"---\ntitle: Figure Maker\ndescription: figure maker\nsection: Viewer\norder: 27\n---\n\n\n# Figure Maker\n##### [add-on]\n\nFigure Maker extends the capabilities of [Split View](/docs/viewer/split-view/) for creating publication-ready Figures. Using Figure Maker it's possible to decorate image panels created with [Split View](/docs/viewer/split-view/) using markup tools and export the result in common formats for use in other applications. Figure Maker reduces the need for image editing software when preparing Figures by providing the ability to:\n\n- Save image panels created with [Split View](/docs/viewer/split-view/)\n- Add markup such as scale bars, text labels, and slide labels to image panels\n- Easily configure the visibility of annotations and image overlays\n- Export image panels in common image formats\n\nTo change the color management profile
\n\n 1. Hover or click on the image to reveal the toolbar at the top left of the panel\n\n 2. Click on the  button to expand the toolbar if necessary\n\n 3. Click on the  button dropdown menu in the toolbar to reveal the color management dialog\n\n 4. Select one of the available ICC color profiles\n\n\n The Figure maker add-on is required to create or edit Figures.\n
\n\n\n## Creating a Figure\n\nFigures are created when image panels, that are created using [Split View](/docs/viewer/split-view/), are saved. Therefore, a Figure may have one or more images, the number of images and their arrangement can be adjusted in the usual way, and each image can be individually manipulated (panned, zoomed) or synchronized to find desired ROIs within each panel.\n\nWhen saving a Figure using Figure Maker, the properties that affect the appearance of the Figure are saved including the layout and arrangement of panels, the ROI within each panel and the markup configuration of panels. Panel properties are recorded relative to the current image viewing area.\n\n\n If you attempt to modify an item which is governed by a reason for change tracking policy, you will be required to provide a reason for the change.\n
\n\n
\n\nTo create a Figure from within the Viewer
\n\n 1. Open one or more images in the Viewer to create image panel(s). See [Split View](/docs/viewer/split-view/) for more details\n\n 2. (Optional) Configure the markup for the panel(s). See [Figure Markup](#figure-markup) for more details\n\n 3. Click on the  icon at the right corner of the Viewer top bar\n\n 4. Select **Save As** from the dropdown menu\n\n 5. In the **Save As** dialog that pops up, navigate to a folder using the folder browser\n - Click on the folder name dropdown menu at the top of the dialog to see a list of folders related to the current view, and a list of recently visited folders\n\n 6. Enter a **Name** in the text box at the bottom left\n\n 7. Click on the **Save** button\n\n\n\n Changes that affect the appearance of image panel(s) are saved, including the panel layout, ROI, and markup.\n
\n\n\n\n
\n\nTo save changes made to a Figure
\n\n 1. Make changes to the Figure, such as adding annotations and labels. See [Figure Markup](#figure-markup) for more details\n\n 2. Click on the  icon at the right corner of the Viewer top bar\n\n 3. Select **Save** from the dropdown menu\n\n\n\n Changes that affect the appearance of image panel(s) are saved, including the panel layout, ROI, and markup.\n
\n\n\n\n
\n\nTo open a previously saved Figure
\n\n 1. Navigate to any folder in the Repository (click on the  **Repository** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu) then navigate to a folder)\n\n 2. Click on an item with the  icon or that has the **Type** of \"Figure\" in the file listing\n\n\n\n Figures automatically scale to the on-screen space available to the Viewer/application when opened. While the on-screen size of image panels can change depending on the context, Figure Maker aims to retain the ROI within each panel by scaling the images appropriately (i.e., setting a lower or higher magnification when the on-screen panel dimensions get smaller or larger, respectively).\n
\n\n\n\n
\n\nTo rename a Figure from within the Viewer
\n\n 1. Click on the current name of the Figure at the top left of the Viewer (defaults to \"Untitled View\"), or the  icon next to it\n\n 2. Type the new name for the Figure\n\n\n\n
\n\n\n## Figure Markup\n\nMany of the markup features that are available in the Viewer can be configured for each of the images in the Figure. The markup for each of the image panels can be independently controlled.\n\n\n### Image Annotations\n\nThe annotations that have been previously created can be made visible on an image panel. In addition, new annotations can be created directly from the Figure Maker environment.\n\nTo rename a Figure from the Repository
\n\n 1. Navigate to any folder in the Repository (click on the  **Repository** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu) then navigate to a folder)\n\n 2. Right click on an item with the  icon or that has the **Type** of \"Figure\" in the file listing to bring up the context menu\n\n 3. Click **Rename**\n\n 4. In the popup dialog, type a new name for the Figure\n\n 5. Click on the **Rename** button or press the **Enter** key to save. To discard your changes, click on the **Cancel** button or press the **Escape** key\n\n\n Annotations can only be created when annotations on the panel are visible.\n
\n\n\n\n
\n\nTo toggle the visibility of annotations on an image panel
\n\n 1. Hover or click on the image to reveal the toolbar at the top left of the panel\n\n 2. Click on the  button to expand the toolbar if necessary\n\n 3. Click on the  button to reveal the markup menu\n\n 4. Adjust the **Annotations** toggle to show or hide image annotations\n\n 5. (Optional) Click on **Annotations** to expand the section and click on **Apply to All Slides** to apply the visibility setting to all panels\n\n\n\n Borders of snapshots are not included in exported Figures even when annotations are visible.\n
\n\n\n\n
\n\n\n### Slide Label\n\nThe slide label can be overlaid on an image panel and made visible until it's removed.\n\nTo create annotations on an image panel
\n\n 1. Ensure annotations for the image panel are visible (see above)\n\n 2. Right-click on the image to open up the annotation ring\n\n 3. Select an annotation tool and follow the on-screen instructions to create a new annotation. See [Creating Annotations](/docs/viewer/annotations-panel/#creating-annotations) for more details\n\n\n\n
\n\n\n### Text Label\n\nA text label can be overlaid on an image panel and made visible until it’s removed.\n\nTo toggle the visibility of the slide label on an image panel
\n\n 1. Hover or click on the image to reveal the toolbar at the top left of the panel\n\n 2. Click on the  button to expand the toolbar if necessary\n\n 3. Click on the  button to reveal the markup menu\n\n 4. Adjust the **Slide Label** toggle to show or hide the label\n\n 5. Click on **Slide Label** to expand the section and adjust preferences\n 1. (Optional) Adjust the location of the label by clicking one of the four corners in the control to the right of **Alignment**\n 2. (Optional) Click on the  button to rotate the label\n 3. (Optional) Click on **Apply to All Slides** to apply these settings to all panels\n\n\n\n
\n\n\n### Scale Bar\n\nA scale bar can be overlaid on an image panel and made visible until it’s removed.\n\nTo include a text label on an image panel
\n\n 1. Hover or click on the image to reveal the toolbar at the top left of the panel\n\n 2. Click on the  button to expand the toolbar if necessary\n\n 3. Click on the  button to reveal the markup menu\n\n 4. Adjust the **Label** toggle to show or hide the label\n\n 5. Click on **Label** to expand the section and adjust preferences\n 1. (Optional) Adjust the label text in the field below the toggle (default text will be the image name)\n 2. (Optional) Adjust the location of the label by clicking one of the four corners in the control to the right of **Alignment**\n 3. (Optional) Adjust the text color by clicking in the colored box to the right of **Foreground**, then selecting a color\n 4. (Optional) Adjust the text background color by clicking in the colored box to the right of **Background**, then selecting a color\n 5. (Optional) Click on **Apply to All Slides** to apply these settings to all panels\n\n\n\n
\n\n\n## Downloading Figures\n\nThe contents of a Figure can be exported as a common image format (PNG, JPEG, TIFF, or PDF) for use in presentations or other documents.\n\nTo include a scale bar on an image panel
\n\n 1. Hover or click on the image to reveal the toolbar at the top left of the panel\n\n 2. Click on the  button to expand the toolbar if necessary\n\n 3. Click on the  button to reveal the markup menu\n\n 4. Adjust the **Scale Bar** toggle to show or hide the scale bar\n\n 5. Click on **Scale Bar** to expand the section and adjust preferences\n 1. (Optional) Adjust the location of the scale bar by clicking one of the four corners in the control to the right of **Alignment**\n 2. (Optional) Adjust the text and scale bar color by clicking in the colored box to the right of **Color**, then selecting a color\n 3. (Optional) Adjust the **Show measurement text** toggle to show or hide the measurement\n 4. (Optional) Adjust the **Show border** toggle to show or hide a border around the text and scale bar\n 5. (Optional) Adjust the **Automatic length** toggle to determine the size of the scale bar\n - When enabled the size is determined automatically\n - When disabled the user can specify the size of the scale bar and select a unit of measurement from the dropdown menu\n 6. (Optional) Select the location of the measurement text relative to the scale bar by clicking one of the **Text Alignment** options:  (left),  (center), or  (right)\n 7. (Optional) Click on **Apply to All Slides** to apply these settings to all panels\n\n\n\n
\n\nTo export a Figure from the Repository
\n\n 1. Navigate to any folder in the Repository (click on the  **Repository** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu) then navigate to a folder)\n\n 2. Select a Figure object from the folder listing\n\n 3. Bring up the context menu for the item\n\n 4. Click on **Export Figure** to bring up the **Download Figure** popup dialog\n\n 5. Click on the **Download** menu at the bottom right of the dialog\n\n 6. Adjust preferences such as\n - **Size**: adjust the width or height to specify the desired size\n - **File type**: select the desired format from the dropdown menu\n - **White Background**: Enable to use a white background instead of the default black in the exported image\n\n 7. Click on the **Download** button\n\n 8. If prompted, select a location to save the downloaded file\n\n\n\n
\n\n\n## Deleting Figures\n\nFigures can be moved to the [Trash](/docs/repository/trash/) from the Repository.\n\nTo export a Figure from within the Viewer
\n\n 1. Create a new Figure or open an existing Figure in the Viewer\n\n 2. Click on the  button in the Viewer top bar to display the Download dialog\n\n 3. Adjust preferences such as\n - **Size**: adjust the width or height to specify the desired size\n - **File type**: select the desired format from the dropdown menu\n - **White Background**: Enable to use a white background instead of the default black in the exported image\n\n 4. Click on the **Download** button\n\n 5. If prompted, select a location to save the downloaded file\n\n\n\n
\n","slug":"docs/viewer/figure-maker"},{"frontmatter":{"title":"Annotations Panel","description":"annotations panel"},"rawBody":"---\ntitle: Annotations Panel\ndescription: annotations panel\nsection: Viewer\norder: 22\n---\n\n\n# Annotations Panel\n\nTo move a Figure to the Trash from the Repository
\n\n 1. Navigate to any folder in the Repository (click on the  **Repository** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu) then navigate to a folder)\n\n 2. Select a Figure object from the folder listing\n\n 3. Bring up the context menu for the item\n\n 4. Click on **Move to Trash**\n\n 5. Click on the **Yes** button to confirm\n\n\n\nThe Annotations panel contains a list of all geometric annotations that have been drawn onto the image and allows the user to modify many of their properties.\n\n
\n\n
\n\nTo toggle the visibility of the Annotations panel
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Click on the  button in the left sidebar to open the Annotations panel\n\n\n\n
\n\n\n## Creating Annotations\n\nTo resize the Annotations panel
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. Click and drag the right border of the panel to resize it\n\n\n\n
\n\nThe following annotation types are available:\n\n| Tool | Instruction to create |\n| -------- | ------------------------------------------------------------ |\n| Rect | Click and drag to contain an area of interest. |\n| Arrow | Click and drag to point to an area of interest. The starting point will be the arrowhead. |\n| Polygon | Click to add points.To create annotations
\n\n 1. From within the Viewer, right-click on an image to open up the annotation ring\n\n 2. Select an annotation tool\n\n 3. Follow the on-screen instructions at the top of the Viewer to draw\n\n 4. Follow the on-screen instructions at the top of the Viewer to end drawing\n\nClick on the first point to close (end) the drawing or press **Z** to close automatically.
Press **Ctrl + Z** to undo the last point.
To pan while drawing, hold the **Shift** key and drag with the mouse. |\n| Freehand | Click and drag to draw on the image. |\n| Ruler | Click and drag to measure the area of interest. |\n| Ellipse | Click and drag to contain the area of interest. The starting point will be the center of the ellipse. |\n| Bookmark | Click to place a bookmark pin on the image. |\n\n\n## Editing Annotations\n\n
\n If you attempt to modify an item which is governed by a reason for change tracking policy, you will be required to provide a reason for the change.\n
\n\n
\n\n#### Resizing Annotations\n\nAll annotation types except for bookmarks can be resized.\n\nTo move an annotation
\n\n 1. Select an annotation to reveal its control points by clicking the border of the rectangle, ellipse or other shape\n\n 2. Click and drag the shape to move it around the Viewer\n\n\n\n
\n\n#### Moving Individual Annotation Points\n\nIndividual points can only be changed for polygon and freehand annotations.\n\nTo resize an annotation
\n\n 1. Select an annotation to reveal its control points by clicking the border of the rectangle, ellipse or other shape\n\n 2. (Optional) Hold down the **Ctrl** key on the keyboard to maintain the current aspect ratio of the shape\n\n 3. Click and drag the control points to adjust the annotation width (side points), height (top and bottom points), or both (corner points)\n\n\n\n
\n\n### Properties\n\nThe following annotation properties can be changed from the Annotations panel or by clicking on the annotation in the Viewer, which exposes a popup dialog.\n\n#### Annotation Color\n\nThere are 6 possible colors for annotations, these can be changed from within the Viewer or from the Annotations panel.\n\nTo change an annotation's individual points
\n\n 1. Double click the border of a polygon or freehand shape to reveal its individual points\n\n 2. Click and drag the points to adjust the annotation\n\n\n\n
\n\nTo change an annotation color from within the Viewer
\n\n 1. Select an annotation to reveal a dialog by clicking the border of the rectangle, ellipse or other shape\n\n 2. Click on the solid circle at the top right of the popup dialog\n\n 3. Select one of the available colors\n\n\n\n
\n\n\n#### Annotation Name\n\nThe name is a single line text field that supports unicode characters. The name is displayed on the annotation and can be changed from within the Viewer or from the Annotations panel.\n\nTo change an annotation color from the Annotations panel
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. Identify the annotation entry to be modified\n\n 4. Click on the solid circle at the top right of the entry\n\n 5. Select one of the available colors\n\n\n\n
\n\nTo rename an annotation from within the Viewer
\n\n 1. Select an annotation to reveal a dialog by clicking the border of the rectangle, ellipse or other shape\n\n 2. Click on the first line of text in the popup dialog (default: \"Untitled\")\n\n 3. Provide a name or edit the existing text\n\n 4. Press the **Enter** key or click away from the textbox to save your changes\n\n\n\n
\n\n\n#### Annotation Description\n\nThe description is a multiline text field that supports unicode characters and can be modified from within the Viewer or from the Annotations panel. Enter new lines by pressing **Shift + Enter**.\n\nTo rename an annotation from the Annotations panel
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. Identify the annotation entry to be modified\n\n 4. Click on the first line of text in the entry (default: \"Untitled\")\n\n 5. Provide a name or edit the existing text\n\n 6. Press the **Enter** key or click away from the textbox to save your changes\n\n\n\n
\n\nTo edit an annotation description from within the Viewer
\n\n 1. Select an annotation to reveal a dialog by clicking the border of the rectangle, ellipse or other shape\n\n 2. Click on the second line of text in the popup dialog (default: \"No description\")\n\n 3. Provide a description or edit the existing text\n\n 4. Press the **Enter** key or click away from the textbox to save your changes\n\n\n\n
\n\n\n#### Annotation Visibility\n\nAnnotations are visible on the image by default once drawn. If you need to declutter the image, you may hide individual annotations or all annotations at once.\n\nTo edit an annotation description from the Annotations panel
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. Identify the annotation entry to be modified\n\n 4. Click on the second line of text in the entry (default: \"No description\")\n\n 5. Provide a description or edit the existing text\n\n 6. Press the **Enter** key or click away from the textbox to save your changes\n\n\n\n
\n\nTo change the visibility of individual annotations
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. Identify the annotation entry to be modified\n\n 4. Click on the  button to toggle visibility\n\n\n\n
\n\n\n#### Annotation Sharing\n\nAnnotations may be shared with your team or kept private for the user that created them. Shared annotations are visible to all users in your team while private annotations are only visible to the user that created them.\n\nBy default, annotations are created as shared annotations. This preference can be changed from the Annotations panel by toggling the / button at the top right corner of the Annotations panel.\n\nTo change the visibility of all annotations
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. Click on the  button at the top right corner of the Annotations panel to toggle visibility for all annotations\n\n\n\n
\n\n\n### Locating an Annotation\n\nWhile on the Viewer, annotations are easily visible and accessible.\n\nTo toggle the sharing mode for individual annotation
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. Identify the annotation entry to be modified\n\n 4. Click on the  **Shared**/ **Private** button to toggle the annotation’s sharing mode\n\n\n\n
\n\n\n## Deleting Annotations\n\nAnnotations can be deleted from within the Viewer or from the Annotations panel.\n\nTo locate a corresponding annotation object (on the image) from the Annotations panel
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. Identify the annotation entry\n\n 4. Click on the  button to jump to the annotation in the Viewer\n\n\n\n
\n\nTo delete an annotation from within the Viewer
\n\n 1. Select an annotation to reveal a dialog by clicking the border of the rectangle, ellipse or other shape\n\n 2. Click on the  button at the bottom right of the popup dialog\n\n 3. Click on the **OK** button to confirm\n\n\n\n
\n","slug":"docs/viewer/annotations-panel"},{"frontmatter":{"title":"Browse Folder Panel","description":"browse folder panel"},"rawBody":"---\ntitle: Browse Folder Panel\ndescription: browse folder panel\nsection: Viewer\norder: 18\n---\n\n\n# Browse Folder Panel\n\nTo delete an annotation from the Annotations panel
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. Identify the annotation entry to be deleted in the list\n\n 4. Click on the  button\n\n 5. Click on the **OK** button to confirm\n\n\n\nThe Browse Folder panel displays the list of images in the same folder as the file currently on display in the Viewer. You can view the images in List view, Icon view or Compact List view. The Browse Folder panel can be accessed by clicking the  button located on the left-hand sidebar of the Viewer.\n\n
\n\n
\n\nTo toggle the visibility of the Browse Folder panel
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Click on the  button in the left sidebar to open the Browse Folder panel\n\n\n\n
\n\nTo resize the Browse Folder panel
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. Click and drag the right border of the panel to resize it\n\n\n\n
\n\nTo open the current image's folder
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. Click on the folder name at the top of the panel\n\n\n\n
\n\n\n## List Mode\n\nThe Browse Folder panel can list items using three formats: List, Compact List, and Icon.\n\nTo open the current image's folder in a new browser tab
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. Click on the  button to the right of the folder name\n\n\n\n
\n\n\n## Sort Order\n\nThe list of items in the Browse Folder panel can be sorted by any metadata field.\n\nTo change the list mode
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. Click on the **Display Mode** button at the top right of the item list. This button will appear different depending on the current display mode: List (), Compact List (), or Icon ()\n\n 4. Click on the desired list view mode\n\n 5. (Optional) Toggle the display of image labels in the list by clicking on **Show Labels**\n\n\n\n
\n\n\n## Name Filter\n\nThe list of items can be filtered by name for quicker browsing.\n\nTo change the sort order
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. Click on the sort order dropdown menu at the top right of the list of files. It shows the currently selected field by which it is sorting (defaults to \"Name\")\n\n 4. (Optional) Click on the arrow immediately to the right of the field name to toggle between sorting in  ascending order or  descending order\n\n\n\n \n\n
\n\n\n## File Read Status\n\nThe file read status indicates if a file has been previously clicked on (i.e., viewed) by the currently logged-in user. An unread status is indicated by a boldface font in the Browse Folder panel and the read status is indicated by a plain face font.\n\nTo filter the list
\n\n 1. Click in the search box indicated by the  icon and the text \"Filter by name...\"\n\n 2. Type in the filter you wish to apply to the names. Only the items matching this text will be displayed\n\n\n\n The filter can include one or more wildcard characters (
*) which matches any character zero or more times.\n \n\n
\n\nTo toggle the read status
\n\n 1. Bring up the [context menu](/docs/repository/repository-operations/#context-menu) for any entry in the Browse Folder panel\n\n 2. Click **Mark as Read** to enable the read status, or\n\n 3. Click **Mark as Unread** to clear the read status\n\n\n\n
\n\n\n## File Favorite Status\n\nAny file that has been tagged as _Starred_ by the currently logged-in user is considered a favorite. Items tagged this way are quickly and easily accessible from the Starred Items List, and are indicated by a solid star in the Browse Folder panel.\nSee [Favorite Status](/docs/repository/repository-operations/#favorite-status) for more details.\n\nTo toggle the read status on multiple items
\n\n 1. Select one or more items by holding the **Ctrl** key (on Windows) or **⌘ / Command** key (on macOS) key and clicking on them\n\n 2. Click the **# Selected** dropdown menu which appears at the top left of the list of files\n\n 3. Click **Mark as Read** to enable the read status, or\n\n 4. Click **Mark as Unread** to clear the read status\n\n\n\n
\n\nTo toggle the favorite status
\n\n 1. Click on the  button to the left of an item name in the Browse Folder panel to add the _Starred_ tag, or\n\n 2. Click on the  button to the left of an item name in the Browse Folder panel to remove the tag\n\n\n\n
\n","slug":"docs/viewer/browse-folder-panel"},{"frontmatter":{"title":"Help Panel","description":"help panel"},"rawBody":"---\ntitle: Help Panel\ndescription: help panel\norder: 25\nsection: Viewer\n---\n\n\n# Help Panel\n\nTo toggle the favorite status on multiple items
\n\n 1. Select one or more items by holding the **Ctrl** key (on Windows) or **⌘ / Command** key (on macOS) key and clicking on them\n\n 2. Click the **# Selected** dropdown menu which appears at the top left of the list of files\n\n 3. Click **Favorite** to add the _Starred_ tag, or\n\n 4. Click **Unfavorite** to remove the tag\n\n\n\nThe Help panel provides a quick and convenient reference for mouse actions and keyboard shortcuts within the Viewer.\n\nIt also includes a color guide for the [Overview Tool Heatmap](/docs/viewer/overview-tool/#heatmap).\n\n
\n\n
\n\nTo toggle the visibility of the Help panel
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Click on the  button in the left sidebar to open the Help panel\n\n\n\n
\n","slug":"docs/viewer/help-panel"},{"frontmatter":{"title":"Image Adjustments Panel","description":"image adjustments panel"},"rawBody":"---\ntitle: Image Adjustments Panel\ndescription: image adjustments panel\norder: 20\nsection: Viewer\n---\n\n\n# Image Adjustments Panel\n\nTo resize the Help panel
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. Click and drag the right border of the panel to resize it\n\n\n\nThe Image Adjustments panel can be used to add basic filters to an image.\n\n
\n\n
\n\nTo toggle the visibility of the Image Adjustments panel
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Click on the  button in the left sidebar to open the Image Adjustments panel\n\n\n\n
\n\nTo resize the Image Adjustments panel
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Click on the  button in the left sidebar to open the Image Adjustments panel\n\n 3. Click and drag the right border of the panel to resize it\n\n\n\n
\n\nTo add a filter to an image
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Click on the  button in the left sidebar to open the Image Adjustments panel\n\n 3. Click on the icon of the desired filter and make adjustments. See [Filters](#filters) for more details\n\n\n\n
\n\nTo change the order in which filters are applied
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Click on the  button in the left sidebar to open the Image Adjustments panel\n\n 3. Click on the  or  to the right of the filter name to move it up or down the list\n\n\n\n The image filters are applied in order from top to bottom.\n
\n\n\n\n
\n\n\n## Filters\n\nThe following filters can be applied to an image. These only apply to the image as it is displayed in the Viewer, not the underlying image data.\n\n###  Contrast\n\nThe contrast filter allows you to change the apparent contrast of the displayed image. Negative values reduce the contrast while positive values increase it.\n\nThe slider sets the adjustment value in the range \\[-255, 255\\] with a default value of 0.\n\n###  Brightness\n\nThe brightness filter adjusts the displayed image by adding a constant value to the pixel intensities.\n\nThe slider sets the adjustment value in the range \\[-255, 255\\] with a default value of 0.\n\n###  Threshold\n\nThe threshold filter converts the entire image to black and white. Pixels with an average intensity below the threshold value are converted to black and all others are converted to white.\n\nThe slider sets the threshold value in the range [0, 255] with a default value of 128.\n\n###  Invert\n\nThe invert filter inverts the colors displayed in the image.\n\n###  Window\n\nThe window filter converts the image to grayscale and scales all of the intensity values to fit within the configured range of values.\n\nThe **Center** slider determines the midpoint of the range of valid values. This slider is in the range [0 - 256] with a default value of 128.\n\nThe **Width** slider sets the upper and lower bounds of the range of valid values; half of the width below the **Center** and half above. This slider is in the range [1 - 256] with a default value of 256.\n\n###  Isolate\n\nThe isolate filter allows you to display one of the red, green, or blue channels of the image as grayscale.\n\nThe **Channel** slider can be adjusted to 0 (red), 1 (green), or 2 (blue).\n","slug":"docs/viewer/image-adjustments-panel"},{"frontmatter":{"title":"Image Settings Panel","description":"image settings panel"},"rawBody":"---\ntitle: Image Settings Panel\ndescription: image settings panel\norder: 19\nsection: Viewer\n---\n\n\n# Image Settings Panel\n##### \\[BioPharma] [Research+]\n\nThe Image Settings panel can be used to alter how images in the Viewer are rendered, including adjusting the individual channels of multi-channel images. These settings are saved as preferences for the current user, with the option to name the collection of settings, apply them to other images, and share them with your team.\n\nTo remove a filter currently applied to the image
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Click on the  button in the left sidebar to open the Image Adjustments panel\n\n 3. Click on the **X** to the right of the filter name to remove it from the list\n\n\n\n
\n\nTo toggle the visibility of the Image Settings panel
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Click on the  button in the left sidebar to open the Image Settings panel\n\n\n\n
\n\n\n## Controls\n\n### Context Menu\n\nMany operations in the various dialogs are performed via a context menu. This menu is accessed by right-clicking on an item in the list (or one of the currently selected items when using [Multi-Select](#multi-select)).\n\nTo resize the Image Settings panel
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. Click and drag the right border of the panel to resize it\n\n\n On a mobile device, tap and hold on an item to display the context menu.\n
\n\n### Multi-Select\n\nOne or more items can be selected in a dialog in order to perform operations on items at once.\n\n\n\n
\n\nTo select more than one item
\n\n 1. In the dialog, click on an item in the list\n\n 2. While holding the **Ctrl** key (on Windows) or **⌘ / Command** key (on macOS) select another item\n\n 3. Repeat step 3 as necessary\n\n\n\n
\n\n\n## Image Settings\n\nThe Image Settings panel provides options for adjusting how the currently selected image is rendered, saving those settings, and sharing them with your team.\n\n\n### Managing Image Settings\n\nThe dropdown menu at the top of the Image Settings panel can be used to select and apply to the current image a previously saved collection of settings, some of which may be [shared from other members of your team](#sharing-settings-with-your-team).\n\nBy default, the list of saved settings is displayed with those you have set as [preferred](#preferred-settings) at the top, followed by the remaining options sorted by creation date in descending order. You may also set this order manually in the **Saved Settings** dialog.\n\nIf you have made any adjustments since you last saved, the dropdown menu will display _Unsaved Settings_.\n\nTo select more than one item in a continuous range
\n\n 1. In the dialog, click on the first item in the range from the list\n\n 2. While holding the **Shift** key, select the last item in the range\n\n\n\n
\n\nTo save the current image settings
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Click on the  button in the left sidebar to open the Image Settings panel\n\n 3. Click on the  button to the right of the dropdown menu at the top of the panel to display the context menu\n\n 4. Click **Save Settings As** in the context menu\n\n 5. Type a name for these settings in the **Name** field\n\n 6. (Optional) Select **Share with Team** to make these settings available to other members of your team\n\n 7. (Optional) Select **Mark as Preferred** to keep this collection of settings at the top of the list\n\n 8. Click on the **Save** button\n\n\n\n Only users with the \"View shared image settings\" permission flag can save sets of image settings.\n
\n\n\n\n
\n\nTo load a previously saved collection of image settings
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Click on the  button in the left sidebar to open the Image Settings panel\n\n 3. Click on the dropdown menu at the top of the panel\n\n 4. (Optional) Begin typing the name of the collection you want to apply to filter the list\n\n 5. Select one of the collections of image settings from the list\n\n\n\n
\n\nTo reset the current image settings to their default values
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Click on the  button in the left sidebar to open the Image Settings panel\n\n 3. Click on the  button to the right of the dropdown menu at the top of the panel to display the context menu\n\n 4. Click **Apply Default Image Settings** in the context menu\n\n\n\n
\n\nTo change the order that image settings appear in the dropdown menu
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Click on the  button in the left sidebar to open the Image Settings panel\n\n 3. Click on the  button to the right of the dropdown menu at the top of the panel to display the context menu\n\n 4. Click **Manage Settings** in the context menu\n\n 5. In the **Saved Settings** dialog that pops up, move an item up and down by clicking on the  handle to the left of the name and dragging it to the new position\n\n\n\n
\n\n\n### Copying Image Settings\n##### [BioPharma]\n\nImage settings can be copied from one image to another, or to a folder. Copying to a folder makes the settings available to all of the images in that folder.\n\nWhen settings are copied to another image, the collection of values for black point, white point, brightness, gamma, and visible channels is added to the dropdown menu of the target image under a name of your choosing. You can also set these settings as preferred or share them with your team at the same time.\n\nTo delete a saved collection of image settings
\n\n\n Deleting a collection of image settings you have shared removes it for everyone on your team.\n
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Click on the  button in the left sidebar to open the Image Settings panel\n\n 3. Click on the  button to the right of the dropdown menu at the top of the panel to display the context menu\n\n 4. Click **Manage Settings** in the context menu\n\n 5. [Select one or more](#multi-select) items to delete in the **Saved Settings** dialog that pops up\n\n 6. Bring up the [context menu](#context-menu) for the item (or items)\n\n 7. Click **Delete** in the context menu\n\n 8. Click on the **Yes** button to confirm\n\n\n Transferring settings may not deliver the expected results if target and source files have different numbers of sub-images or channels within each sub-image. Therefore, this feature works best for files that use a similar scanning protocol.\n
\n\n\n\n
\n\nTo copy the currently applied image settings to another image
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Click on the  button in the left sidebar to open the Image Settings panel\n\n 3. Click on the  button to the right of the dropdown menu at the top of the panel to display the context menu\n\n 4. Hover over **Copy Settings To** in the context menu to expand that menu\n\n 5. Click **Files** in the expanded menu to display the **Copy Settings To** dialog\n\n 6. Locate the image to which you wish to copy these settings\n\n 7. (Optional) Type a name for these settings in the **Name** field at the bottom left. Leaving this field blank will retain the current name\n\n 8. (Optional) Enable **Share with Team** to also [share these settings with your team](#sharing-settings-with-your-team)\n\n 9. (Optional) Enable **Mark as Preferred** to also mark these settings as [preferred](#preferred-settings)\n\n 10. Click on the **Apply** button\n\n\n\n
\n\nTo copy the currently applied image settings to a folder
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Click on the  button in the left sidebar to open the Image Settings panel\n\n 3. Click on the  button to the right of the dropdown menu at the top of the panel to display the context menu\n\n 4. Hover over **Copy Settings To** in the context menu to expand that menu\n\n 5. Click **Folder** in the expanded menu to display the **Copy Settings To** dialog\n\n 6. Locate the folder to which you wish to copy these settings\n\n 7. (Optional) Type a name for these settings in the **Name** field at the bottom left. Leaving this field blank will retain the current name\n\n 8. (Optional) Enable **Share with Team** to also [share these settings with your team](#sharing-settings-with-your-team)\n\n 9. (Optional) Enable **Mark as Preferred** to also mark these settings as [preferred](#preferred-settings)\n\n 10. (Optional) Enable **Apply Recursively** to copy these settings to all images and folders contained in subfolders (and subfolders of those folders, etc.) of the target folder instead of just the direct children\n\n 11. Click on the **Apply** button\n\n\n\n
\n\nTo copy a saved collection of image settings to another image
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Click on the  button in the left sidebar to open the Image Settings panel\n\n 3. Click on the  button to the right of the dropdown menu at the top of the panel to display the context menu\n\n 4. Click **Manage Settings** in the context menu\n\n 5. [Select one or more](#multi-select) items to copy in the **Saved Settings** dialog that pops up\n\n 6. Bring up the [context menu](#context-menu) for the item (or items)\n\n 7. Hover over **Copy Settings To** in the context menu to expand that menu\n\n 8. Click **Files** in the expanded menu to display the **Copy Settings To** dialog\n\n 9. Locate the image to which you wish to copy these settings\n\n 10. (Optional) Type a name for these settings in the **Name** field at the bottom left. Leaving this field blank will retain the current name\n\n 11. (Optional) Enable **Share with Team** to also [share these settings with your team](#sharing-settings-with-your-team)\n\n 12. (Optional) Enable **Mark as Preferred** to also mark these settings as [preferred](#preferred-settings)\n\n 13. Click on the **Apply** button\n\n\n\n
\n\n\n### Applying Image Settings\n##### [BioPharma]\n\nYou also have the option to apply a set of image channel adjustments to another image, or an entire folder. Like copying, applying the settings to a folder applies them to all of the images in that folder.\n\nThe apply action will transfer channel settings from each sub-image of the source file to the same channel and sub-image of the target file (i.e., matching is performed using the sub-image and channel indices). For example, when transferring settings from \"Image A\" to \"Image B\": the values for channel index _i_ of sub-image _j_ will be transferred from \"Image A\" to the same indices in \"Image B\", for the range of _i_ and _j_ that is valid (exist) in both files.\n\nTo copy a saved collection of image settings to a folder
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Click on the  button in the left sidebar to open the Image Settings panel\n\n 3. Click on the  button to the right of the dropdown menu at the top of the panel to display the context menu\n\n 4. Click **Manage Settings** in the context menu\n\n 5. [Select one or more](#multi-select) items to copy in the **Saved Settings** dialog that pops up\n\n 6. Bring up the [context menu](#context-menu) for the item (or items)\n\n 7. Hover over **Copy Settings To** in the context menu to expand that menu\n\n 8. Click **Folder** in the expanded menu to display the **Copy Settings To** dialog\n\n 9. Locate the folder to which you wish to copy these settings\n\n 10. (Optional) Type a name for these settings in the **Name** field at the bottom left. Leaving this field blank will retain the current name\n\n 11. (Optional) Enable **Share with Team** to also [share these settings with your team](#sharing-settings-with-your-team)\n\n 12. (Optional) Enable **Mark as Preferred** to also mark these settings as [preferred](#preferred-settings)\n\n 13. (Optional) Enable **Apply Recursively** to copy these settings to all images and folders contained in subfolders (and subfolders of those folders, etc.) of the target folder instead of just the direct children\n\n 14. Click on the **Apply** button\n\n\n Image channel names are not used for matching, nor are they copied.\n
\n\n\n\n
\n Transferring settings may not deliver the expected results if target and source files have different numbers of sub-images or channels within each sub-image. Therefore, this feature works best for files that use a similar scanning protocol.\n
\n\n\n\n
\n Some image formats (e.g., SVS, MRXS) have a single sub-image while other formats (e.g., CZI, VSI) may have multiple sub-images, where sub-images are specific ROIs that have been imaged within the scan area. SVS and MRXS use a single sub-image spanning the complete scan area while CZI and VSI may use multiple sub-images to sparsely image the scan area.\n
\n\n\n\n
\n\nTo apply the currently applied image settings to another image
\n\n\n This will replace any currently applied image settings for the target image, but not copy the named collection to that image's saved settings.\n
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Click on the  button in the left sidebar to open the Image Settings panel\n\n 3. Click on the  button to the right of the dropdown menu at the top of the panel to display the context menu\n\n 4. Hover over **Apply Settings To** in the context menu to expand that menu\n\n 5. Click **Files** in the expanded menu to display the **Apply Settings To** dialog\n\n 6. Locate the image to which you wish to apply these settings\n\n 7. Click on the **Apply** button\n\n\n\n
\n\nTo apply the currently applied image settings to a folder
\n\n\n This will replace any currently applied image settings for the target images, but not copy the named collection to those images' saved settings.\n
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Click on the  button in the left sidebar to open the Image Settings panel\n\n 3. Click on the  button to the right of the dropdown menu at the top of the panel to display the context menu\n\n 4. Hover over **Apply Settings To** in the context menu to expand that menu\n\n 5. Click **Folder** in the expanded menu to display the **Apply Settings To** dialog\n\n 6. Locate the folder to which you wish to apply these settings\n\n 7. (Optional) Enable **Apply Recursively** to apply these settings to all images and folders contained in subfolders (and subfolders of those folders, etc.) of the target folder instead of just the direct children\n\n 8. Click on the **Apply** button\n\n\n\n
\n\n
\n\nTo apply a saved collection of image settings to another image
\n\n\n This option is not available when multiple items are selected.\n
\n\n \n\n
\n This will replace any currently applied image settings for the target image, but not copy the named collection to that image's saved settings.\n
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Click on the  button in the left sidebar to open the Image Settings panel\n\n 3. Click on the  button to the right of the dropdown menu at the top of the panel to display the context menu\n\n 4. Click **Manage Settings** in the context menu\n\n 5. In the **Saved Settings** dialog that pops up, locate the settings to apply and bring up the [context menu](#context-menu)\n\n 6. Hover over **Apply Settings To** in the context menu to expand that menu\n\n 7. Click **Files** in the expanded menu to display the **Apply Settings To** dialog\n\n 8. Locate the image to which you wish to apply these settings\n\n 9. Click on the **Apply** button\n\n\n\n
\n\n
\n\n\n### Preferred Settings\n\nIn order to make a previously saved collection of image settings more readily available, you can mark it as preferred. By default, preferred image settings are listed first in the dropdown menu for quick access. These preferred saved settings are also easily identified by the  icon next to their name in both the dropdown menu and **Saved Settings** dialog.\n\nTo apply a saved collection of image settings to a folder
\n\n\n This option is not available when multiple items are selected.\n
\n\n \n\n
\n This will replace any currently applied image settings for the target images, but not copy the named collection to those images' saved settings.\n
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Click on the  button in the left sidebar to open the Image Settings panel\n\n 3. Click on the  button to the right of the dropdown menu at the top of the panel to display the context menu\n\n 4. Click **Manage Settings** in the context menu\n\n 5. In the **Saved Settings** dialog that pops up, locate the settings to apply and bring up the [context menu](#context-menu)\n\n 6. Hover over **Apply Settings To** in the context menu to expand that menu\n\n 7. Click **Folder** in the expanded menu to display the **Apply Settings To** dialog\n\n 8. Locate the folder to which you wish to apply these settings\n\n 9. (Optional) Enable **Apply Recursively** to apply these settings to all images and folders contained in subfolders (and subfolders of those folders, etc.) of the target folder instead of just the direct children\n\n 10. Click on the **Apply** button\n\n\n Only users with the \"Share image settings\" permission flag are able to change the preferred status of image settings.\n
\n\n\n\n
\n\nTo toggle the preferred status of the currently applied image settings
\n\n\n Image settings must be saved before they can be set as preferred.\n
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Click on the  button in the left sidebar to open the Image Settings panel\n\n 3. Click on the  button to the right of the dropdown menu at the top of the panel to display the context menu\n\n 4. Click **Set as Preferred**/**Unset as Preferred** in the context menu to toggle the preferred status of these settings\n\n\n\n
\n\nTo set a saved collection of image settings as preferred
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Click on the  button in the left sidebar to open the Image Settings panel\n\n 3. Click on the  button to the right of the dropdown menu at the top of the panel to display the context menu\n\n 4. Click **Manage Settings** in the context menu\n\n 5. In the **Saved Settings** dialog that pops up, locate the desired item and bring up the [context menu](#context-menu)\n\n 6. Click **Set as Preferred**/**Unset as Preferred** in the context menu to toggle the preferred status of these settings\n\n\n Marking a collection of settings as preferred applies for all team members if the collection is shared.\n
\n\n\n### Sharing Settings With Your Team\n\nOnce saved, a collection of image settings can be shared with other users on your team. This allows multiple people to review an image with consistent adjustments applied. And when combined with the ability to apply these settings to a folder, this provides a convenient method of maintaining consistency across an entire data set.\n\nShared image settings can be identified by the  icon next to their name in both the dropdown menu and **Saved Settings** dialog. Additionally, the avatar of the user who saved these settings is displayed to the left of the entry in these listings. Hovering over the avatar shows you the user's name.\n\n\n Only users with the \"Share image settings\" permission flag are able to share their private settings with their team.\n
\n\n\n\n
\n\nTo share the currently applied image settings with your team
\n\n\n Image settings must be saved before they can be shared.\n
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Click on the  button in the left sidebar to open the Image Settings panel\n\n 3. Click on the  button to the right of the dropdown menu at the top of the panel to display the context menu\n\n 4. Click **Share with Team/Unshare with Team** in the context menu to toggle whether or not the current settings are shared with your team\n\n\n\n
\n\nTo share a saved collection of image settings with your team
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Click on the  button in the left sidebar to open the Image Settings panel\n\n 3. Click on the  button to the right of the dropdown menu at the top of the panel to display the context menu\n\n 4. Click **Manage Settings** in the context menu\n\n 5. In the **Saved Settings** dialog that pops up, locate the desired item and bring up the [context menu](#context-menu)\n\n 6. Click **Share with Team/Unshare with Team** in the context menu to toggle whether or not the current settings are shared with your team\n\n\n\n \n\n
\n\n\n## Histogram\n\nA histogram provides a visual representation of the frequency of intensity values in an image. The histogram in the Viewer plots a separate line for each channel of a multi-channel image, using the same color as the [pseudocolor](#pseudocolor) set in the [Channel List](#channel-list). The horizontal axis of the histogram represents the intensity values and the vertical axis represents the number of pixels of that intensity.\n\nThe histogram can be used to make images more readable to users by allowing them to adjust values such as black point, white point, brightness, and gamma for one or more channels at a time.\n\nTo see sharing details for a collection of image settings
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Click on the  button in the left sidebar to open the Image Settings panel\n\n 3. Click on the dropdown menu at the top of the panel\n\n 4. Hover over the  icon next to a name to show a tooltip which includes the user who shared it and the date it was created\n\n\n\n The share icon in the Saved Settings dialog can also be used in this way.\n
\n\n \n\n
\n\nTo change the channel group
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Click on the  button in the left sidebar to open the Image Settings panel\n\n 3. Select an option from the **Channel Group** dropdown menu. See [Channel Group](#channel-group) for more details\n\n\n\n The channel group determines which channels are affected by histogram adjustments, not which channels are displayed. To change the channels which are plotted in the histogram, see Channels Displayed in the Histogram Options dialog.\n
\n\n
\n\nTo see values in the histogram
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Click on the  button in the left sidebar to open the Image Settings panel\n\n 3. Hover over any location in the histogram to display a crosshair with the intensity value connected to the vertical segment and the count of pixels with that value connected to the horizontal segment\n\n When the cursor is hovering over a line representing a channel, that channel name and color is also displayed\n\n\n\n Clicking an image channel line in the histogram highlights the area under the plotted line with the same color.\n
\n\n\n\n
\n\n\n### Histogram Options\n\nThe settings in the **Histogram Options** dialog are used to modify how the histogram in the Image Settings panel is rendered.\n\nTo see the intensity range of the currently displayed histogram
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Click on the  button in the left sidebar to open the Image Settings panel\n\n 3. Hover over the  icon below the histogram to show a tooltip with the currently displayed intensity range\n\n\n\n \n\n 5. Select an option from the **Vertical Axis** dropdown menu to change the scale used for the histogram's vertical axis: either a **Linear Scale** or a **Logarithmic Scale**\n\n 6. Select an option from the **Horizontal Axis** dropdown menu to change the effective width of the histogram (i.e., the range of values for the horizontal axis):\n - **16-bit**: Up to 216 (65,536) different values\n - **14-bit**: Up to 214 (16,384) different values\n - **12-bit**: Up to 212 (4,096) different values\n - **10-bit**: Up to 210 (1,024) different values\n - **8-bit**: Up to 28 (256) different values\n - **Auto Range**: automatically attempt to set the width to a value that fully contains the image intensity range\n\n \n\n 7. Adjust the **Show Gridlines** toggle to show or hide a grid in the background of the histogram\n\n 8. Click on the **X** button at the top right of the **Histogram Options** dialog to close it\n\n\n
\n\n\n### Channel Settings\n\nThe channel settings can be used to adjust how groups of image channels are rendered in the Viewer.\n\nTo change the histogram rendering options
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Click on the  button in the left sidebar to open the Image Settings panel\n\n 3. Click on the  button at the top right corner of the Image Settings panel to display the **Histogram Options** dialog\n\n 4. Select an option from the **Channels Displayed** dropdown menu to change which image channels are plotted in the histogram:\n - **All**: all channels are plotted\n - **Visible**: only plot the channels which are currently visible. See [Channel List](#channel-list) for more details\n\n\n The Channels Displayed option only controls which image channels are plotted in the histogram — it does not affect which channels are modified by adjustments to the histogram. To change which channels are modified, see Channel Group in the Channel Settings dialog.\n
\n A ![\"Warning\"](\"../images/viewer-panel-alert.svg\")
icon is shown to the left of the ![\"Histogram](\"../images/viewer-panel-chart.svg\")
button in the Image Settings panel when the intensity range of the image is greater than the range selected for the horizontal axis.\n
icon is shown to the left of the button in the Image Settings panel when the intensity range of the image is greater than the range selected for the horizontal axis.\n \n All changes are saved automatically.\n
\n\n\n\n
\n\nTo change the channel settings
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Click on the  button in the left sidebar to open the Image Settings panel\n\n 3. Click on the  button to the right of the **Channel Group** dropdown menu to display the **Channel Settings** dialog\n\n 4. Select the appropriate [channel group](#channel-group)\n\n 5. Adjust the [black and white points](#black-and-white-points)\n\n 6. Adjust the [brightness](#brightness)\n\n 7. Adjust the [gamma](#gamma)\n\n 8. (Optional) Undo all changes you have made since opening this dialog by clicking on the **Undo All** button\n\n 9. Click on the **X** button at the top right of the **Channel Settings** dialog to close it\n\n\n\n All changes are saved automatically.\n
\n\n\n A ![\"Varies](\"../images/varies-number.svg\")
icon in a value field or a ![\"Varies](\"../images/varies-percent.svg\")
icon in a percentile field indicates that multiple image channels in the currently selected group have been adjusted independently. Hover over the icon to show a tooltip with the range of values in the channel group.\n
icon in a value field or a icon in a percentile field indicates that multiple image channels in the currently selected group have been adjusted independently. Hover over the icon to show a tooltip with the range of values in the channel group.\n\n A icon is shown to the right of the dropdown menu if any of the channels included in the channel group are not currently visible in the histogram. Click on the icon to open the Histogram Options dialog to change the Channels Displayed.\n
icon is shown to the right of the dropdown menu if any of the channels included in the channel group are not currently visible in the histogram. Click on the icon to open the Histogram Options dialog to change the Channels Displayed.\n\n\n \n\n
\n\n#### Black and White Points\n\nYou can adjust the rendered dynamic range of an image channel (or group of channels) by setting the **Black Point** and **White Point** values. These define the lowest intensity to display — below which is rendered as zero (the black point) — and the highest intensity to display — above which is rendered as the maximum value (the white point). The remaining intensity values are scaled evenly between these two points, improving contrast.\n\nThe valid range for black and white point values is [`0`, `(2 ^ (bits per channel) - 1)`] — the same range as the horizontal axis of the histogram. The number of bits per channel can be adjusted under **Horizontal Axis** in the [Histogram Options](#histogram-options) dialog.\n\nA percentile value sets the black or white point value to exclude the respective intensity values from the left- or right-hand side of the channel histogram. For example:\n- A 99.99% threshold for white point sets the white point to a value that eliminates 0.01% of pixels from the right-hand side of the histogram\n- A 2% threshold for black point sets the black point to a value that eliminates 2% of pixels from the left-hand side of the histogram\n\nTo change which image channel group is affected by adjustments to the histogram
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Click on the  button in the left sidebar to open the Image Settings panel\n\n 3. Select an option from the **Channel Group** dropdown:\n - **All**: All image channels\n - **Visible**: Only those image channels which are visible in the Viewer. See [Channel Visibility](#channel-visibility) for more details on toggling the visibility of individual channels\n - **Selected**: Only those image channels which are currently selected in the [Channel List](#channel-list)\n - **(Names)**: The remaining items in the dropdown menu refer to the names of image channels in the current image. All image channels which share the name are affected.\n\n\n\n The Channel Group dropdown menu is also available in the Channel Settings dialog.\n
\n Changing either the value or the percentile value for these settings automatically updates the other.\n
\n\n\n\n
\n\nTo manually adjust the black and white points for the current channel group
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Click on the  button in the left sidebar to open the Image Settings panel\n\n 3. Adjust the black point of the current [channel group](#channel-group) by clicking on the / handle to the bottom left of the histogram and dragging it to the right or left\n\n 4. Adjust the white point of the current [channel group](#channel-group) by clicking on the / handle to the bottom right of the histogram and dragging it to the left or right\n\n\n\n The dashed handle indicates that the black or white points of multiple channels in the group have been adjusted independently and have differing values.\n
\n\n\n\n
\n\nTo set the black and white points for an image channel group
\n\n 1. In the **Channel Settings** dialog, select the appropriate [channel group](#channel-group)\n\n 2. Set either the **Black Point** and **White Point** values or their percentile values. Both fields accept numbers with 2 decimal points of precision (e.g., differences as small as 0.01)\n\n 3. (Optional) Click on the  button to the right of the fields to undo changes you have made to the black or white points since opening the **Channel Settings** dialog\n\n 4. Click on the **X** button at the top right of the **Channel Settings** dialog to close it\n\n\n\n All changes are saved automatically.\n
\n\n\n\n \n\n
\n\nTo automatically configure the black and white points for an image channel group
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Click on the  button in the left sidebar to open the Image Settings panel\n\n 3. Select the appropriate option from the [Channel Group](#channel-group) dropdown\n\n 4. Click on the **Best Fit** button below the histogram. This button is also available in the [Channel Settings](#channel-settings) dialog below the black and white point fields\n\n\n\n Best Fit attempts to set the black and white points for each channel in the group individually, using available information in the following order of precedence:
\n
\n
- \n
- The minimum and maximum pixel values derived from the channel histogram \n
- The minimum and maximum pixel values suggested in the image file \n
- The minimum and maximum values supported by the pixel type of each channel \n
\n\n \n\n
\n\nTo reset the black and white points for an image channel group
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Click on the  button in the left sidebar to open the Image Settings panel\n\n 3. Select the appropriate option from the [Channel Group](#channel-group) dropdown\n\n 4. Click on the **Reset** button below the histogram. This button is also available in the [Channel Settings](#channel-settings) dialog below the black and white point fields\n\n\n\n The default values are determined from the following information, in order of precedence:\n
- \n
- The minimum and maximum pixel values suggested in the image file \n
- The minimum and maximum values supported by the pixel type of each channel \n
\n\n
\n\n#### Brightness\n\nThe **Brightness** setting allows you to adjust the brightness of an image by applying an offset to the intensity value of all the pixels of the image. A positive value increases the brightness and a negative value decreases it. This offset is applied linearly (i.e., it is applied equally to all pixels in the image).\n\nThe valid range of values for the brightness setting is [`-1.0`, `1.0`]. This represents a linear scale from `-(2 ^ (bits per channel) -1 )` to `+(2 ^ (bits per channel) -1 )`, with the default value being `0` (no change applied).\n\nTo set the black and white points to their respective minimum and maximum values for an image channel group
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Click on the  button in the left sidebar to open the Image Settings panel\n\n 3. Select the appropriate option from the [Channel Group](#channel-group) dropdown\n\n 4. Click on the **Min/Max** button below the histogram. This button is also available in the [Channel Settings](#channel-settings) dialog below the black and white point fields\n\n\n\n This sets the black and white points to the minimum and maximum values of the histogram's current horizontal axis, respectively.\n
\n\n\n\n
\n\n#### Gamma\n\nThe **Gamma** value allows you to apply gamma correction — a contrast enhancing transform that can be used to improve visualization of poorly exposed images. Unlike the [brightness](#brightness) setting, gamma correction is a nonlinear transform that alters image intensities according to `I’ = Imax (I / Imax)^gamma`. Supported values are in the range of [`0.1`, `3.0`].\n\n\n\nThe gamma correction function is visualized in the histogram as a gray line or curve. If gamma values have been set independently for multiple image channels in the group currently represented in the histogram, then the two curves representing the highest and lowest values are plotted with the area between them highlighted.\n\nTo set the brightness for an image channel group
\n\n 1. In the **Channel Settings** dialog, select the appropriate [channel group](#channel-group)\n\n 2. Adjust the **Brightness** slider to the desired value; or\n\n 3. Click on the number to the right of the slider and type the desired value directly. This field accepts numbers with 2 decimal points of precision (e.g., differences as small as 0.01)\n\n 4. (Optional) Click on the  button to the right of the field to undo changes you have made to the brightness since opening the **Channel Settings** dialog\n\n 5. Click on the **X** button at the top right of the **Channel Settings** dialog to close it\n\n\n\n All changes are saved automatically.\n
\n\n\n\n
\n\nTo set the gamma value for an image channel group
\n\n 1. In the **Channel Settings** dialog, select the appropriate [channel group](#channel-group)\n\n 2. Adjust the **Gamma** slider to the desired value; or\n\n 3. Click on the number to the right of the slider and type the desired value directly. This field accepts numbers with 1 decimal point of precision (e.g., differences as small as 0.1)\n\n 4. (Optional) Click on the  button to the right of the field to undo changes you have made to the gamma since opening the **Channel Settings** dialog\n\n 5. Click on the **X** button at the top right of the **Channel Settings** dialog to close it\n\n\n\n All changes are saved automatically.\n
\n\n\n\n
\n\n\n## Channel List\n\nThe channel list provides controls for toggling the visibility and color of each channel independently or in groups.\n\nThe list shows all sub-images for the current image, numbered starting at zero (`0`). Each sub-image may have zero or more image channels.\n\nTo use a preset gamma value for an image channel group
\n\n 1. In the **Channel Settings** dialog, select the appropriate [channel group](#channel-group)\n\n 2. Click on a button below the **Gamma** slider to use its preset value:\n - **0.45**: The inverse of a common gamma value used by monitors (can be expressed as `1 / 2.2`)\n - **1**: The default value\n - **2.2**: A common gamma value used by monitors\n\n 3. (Optional) Click on the  button to the right of the field to undo changes you have made to the gamma since opening the **Channel Settings** dialog\n\n 4. Click on the **X** button at the top right of the **Channel Settings** dialog to close it\n\n\n The context menu can also be accessed by clicking on x Channels Selected which appears to the right of Channel List.\n
\n\n
\n\n### Channel Visibility\n\nThe visibility of each channel for non-RGB images or sub-images can be controlled independently.\n\nTo filter the channel list
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. Click in the search box indicated by the  icon and the text \"Filter by channel name...\"\n\n 4. Type in all or part of a channel name; only the items matching this text will be displayed in the list below\n\n\n\n
\n\nTo toggle the visibility of an image channel or sub-image
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. Hover over the channel or sub-image you wish to display or hide in the **Channel List**\n\n 4. Click on the / icon to the right of the channel or sub-image name to toggle its visibility\n\n\n\n Sub-images can be distinguished from image channels because all sub-images have the same name as the image file itself and no color assigned.\n
\n\n\n\n
\n\nTo toggle the visibility of all image channels in a sub-image
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. Click on the sub-image name in the **Channel List** to bring up its context menu\n\n 4. Click **Show All Channels** or **Hide All Channels** in the context menu\n\n\n\n
\n\nTo toggle the visibility of a specific selection of image channels
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. [Select one or more](#multi-select) image channels in the **Channel List**\n\n 4. Bring up the [context menu](#context-menu) for the item (or items)\n\n 5. Click **Show Selected** or **Hide Selected** in the context menu\n\n\n\n
\n\nTo hide all image channels except a specific selection
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. [Select one or more](#multi-select) image channels in the **Channel List**\n\n 4. Bring up the [context menu](#context-menu) for the item (or items)\n\n 5. Click **Show Selected Only** in the context menu\n\n\n\n
\n\n\n### Image Channel Properties\n\n#### Name\n\nEach image channel has a name. These are originally set from the image metadata, but can be changed. By setting multiple channels to the same name, they can be grouped and acted upon as one.\n\nTo toggle the visibility of all image channels of a certain type
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. Bring up the [context menu](#context-menu) for a channel in the **Channel List**\n\n 4. Click **Show All <_Name_>** or **Hide All <_Name_>** in the context menu\n\n\n\n All image channels with the same name as the selected item are affected.\n
\n\n\n\n
\n\nTo rename an image channel
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. Click on the name of the channel in the **Channel List**\n\n 4. Type a new name for the channel\n\n 5. Press the **Enter** key or click away from the textbox to save your changes\n\n\n\n
\n\n#### Pseudocolor\n\nEach channel in a multi-channel image is displayed with a pseudocolor, which can be changed to any RGB value.\n\nTo rename several image channels at once
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. [Select one or more](#multi-select) image channels in the **Channel List**\n\n 4. Bring up the [context menu](#context-menu) for the item (or items)\n\n 5. Click **Rename** in the context menu\n\n 6. In the **Rename Channel** dialog that pops up, type a new name for the channels\n\n 7. Click on the **Apply** button or press the **Enter** key to save. To discard your changes, click on the **Cancel** button or press the **Escape** key\n\n\n\n All of the selected channels will share the new name.\n
\n\n\n\n \n\n
\n\nTo change the pseudocolor of an image channel
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. Click on the colored square next to the channel name in the **Channel List** to open the color palette\n\n 4. In the **Edit Color** dialog that pops up, select a color using the palette\n\n 5. Click on the **X** button at the top right of the dialog to close it\n\n\n\n The new color is saved automatically. Click on the Undo Changes button to revert the change.\n
\n\n \n\n
\n\n#### Restoring Default Settings\n\nTo change the pseudocolor of several image channels at once
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. [Select one or more](#multi-select) image channels in the **Channel List**\n\n 4. Bring up the [context menu](#context-menu) for the item (or items)\n\n 5. Click **Edit Color** in the context menu\n\n 6. In the **Edit Color** dialog that pops up, select a color using the palette\n\n 7. Click on the **X** button at the top right of the dialog to close it\n\n\n\n The new color is saved automatically and will apply to all of the selected channels. Click on the Undo Changes button to revert the change.\n
\n\n
\n\nTo reset an image channel name to its default value
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. Locate the channel in the **Channel List**\n\n 4. Click on the  icon to the right of the channel name\n\n 5. Click **Restore Name to Default** in the context menu\n\n\n\n
\n\nTo reset several image channel names
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. [Select one or more](#multi-select) image channels in the **Channel List**\n\n 4. Bring up the [context menu](#context-menu) for the item (or items)\n\n 5. Click **Restore Names to Default** in the context menu\n\n\n\n
\n\nTo reset the pseudocolor of an image channel to its default value
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. Locate the channel in the **Channel List**\n\n 4. Click on the  icon to the right of the channel name\n\n 5. Click **Restore Color to Default** in the context menu\n\n\n\n
\n\nTo reset the pseudocolor of several image channels
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. [Select one or more](#multi-select) image channels in the **Channel List**\n\n 4. Bring up the [context menu](#context-menu) for the item (or items)\n\n 5. Click **Restore Colors to Default** in the context menu\n\n\n\n
\n\nTo reset both the name and color of an image channel to their default values
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. Locate the channel in the **Channel List**\n\n 4. Click on the  icon to the right of the channel name\n\n 5. Click **Restore All to Default** in the context menu\n\n\n\n
\n\n\n### Pixel Value Reporting\n\nIt is possible to enable the display of the value for all visible channels in a multispectral image. When enabled, the intensity of the pixel below the cursor is displayed for each image channel, to the right of its name, in the [Channel List](#channel-list).\n\nTo reset both the name and color of several image channels to their default values
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. [Select one or more](#multi-select) image channels in the **Channel List**\n\n 4. Bring up the [context menu](#context-menu) for the item (or items)\n\n 5. Click **Restore All to Default** in the context menu\n\n\n\n
\n","slug":"docs/viewer/image-settings-panel"},{"frontmatter":{"title":"Image Settings (Legacy)","description":"image settings (legacy)"},"rawBody":"---\ntitle: Image Settings (Legacy)\ndescription: image settings (legacy)\norder: 40\nsection: Viewer\n---\n\n\n# Image Settings (Legacy)\n\nTo enable or disable pixel value reporting
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. Click on the  button to the right of **Channel List** to enable the display of pixel values; or\n\n 4. Click on the  button to disable the feature\n\n\n\nThe Image Settings dialog can be used to alter the rendering of multi-channel images in the Viewer.\n\n
\n The Image Settings dialog has been replaced with the Image Settings Panel, which provides all of the same functionality as well as features not found in this legacy dialog.\n
\n\n
\n Image settings are saved for each user individually. Changes made by one user are not reflected when another user opens the same image.\n
\n\n## Sub-images\n\nThe visibility of [sub-images](/docs/viewer/overview/#sub-images) can be set individually.\n\n\n\n
\n\n\n## Channel Visibility\n\nThe visibility of each channel for non-RGB images or sub-images can be controlled independently. Once these settings are adjusted, they will be saved as preferences for the currently logged-in user.\n\nTo adjust the visibility of sub-images
\n\n 1. From within the Viewer, click on the  button at the bottom left of the Viewer to reveal the Image Settings dialog\n\n 2. Click on the  icon to toggle the visibility of any sub-image\n\n 3. Close the Image Settings dialog by clicking on the **X** button at the top right corner of the popup dialog\n\n\n\n Sub-images can be distinguished from image channels because all sub-images have the same name as the image file itself.\n
\n\n\n\n
\n\n\n## Channel Color Corrections\n\nThere are a number of color correction options available that can be used to alter how a multi-channel image renders on-screen. The values that are shown by default are obtained from the image file itself, if available. Once these settings are adjusted, they will be saved as preferences for the currently logged-in user.\n\nTo adjust the visibility of an image channel
\n\n 1. From within the Viewer, click on the  button at the bottom left of the Viewer to reveal the Image Settings dialog\n\n 2. Click on the  icon to toggle the visibility of any channel\n\n 3. Close the Image Settings dialog by clicking on the **X** button at the top right corner of the popup dialog\n\n\n\n Sub-images can be distinguished from image channels because all sub-images have the same name as the image file itself.\n
\n\n\n Color correction cannot be used on interlaced pixel types (e.g., RGB pixel type commonly used for brightfield images).\n
\n\n\n\n
\n The channels for each sub-image can be adjusted independently.\n
\n\n
\n\nTo change the pseudocolor of a channel
\n\n 1. From within the Viewer, click on the  button at the bottom left of the Viewer to reveal the Image Settings dialog\n\n 2. Click on the colored square next to the channel name to open the color palette\n\n 3. Select a color in the palette\n\n 4. Close the Image Settings dialog by clicking on the **X** button at the top right corner of the popup dialog\n\n\n\n
\n\n\n### Histogram Corrections\n\nThough the histogram is not visible, its properties for each image channel can be adjusted using the following parameters:\n\n- White Point, in the range [0.0, 1.0], is the saturation point on the RHS of the histogram\n- Black Point, in the range [0.0, 1.0], is the saturation point on the LHS of the histogram\n- Gamma, in the range [-2.0, 2.0], is the gamma correction factor\n\nTo reset the pseudocolor of a channel to its default value
\n\n 1. From within the Viewer, click on the  button at the bottom left of the Viewer to reveal the Image Settings dialog\n\n 2. Click on the  button next to the channel name\n\n 3. Close the Image Settings dialog by clicking on the **X** button at the top right corner of the popup dialog\n\n\n\n
\n\nTo adjust the histogram
\n\n 1. From within the Viewer, click on the  button at the bottom left of the Viewer to reveal the Image Settings dialog\n\n 2. Click on the channel name to open a panel of sliders\n\n 3. Adjust any of the sliders\n\n 4. Close the Image Settings dialog by clicking on the **X** button at the top right corner of the popup dialog\n\n\n\n
\n\n\n#### Auto Scale\n\nThe \"Auto Scale\" feature automatically configures the black and white points of multispectral images based on the dynamic range of each channel. This can be used to improve contrast and establish baseline values for the black and white points quickly.\n\nTo reset the histogram to its default value
\n\n 1. From within the Viewer, click on the  button at the bottom left of the Viewer to reveal the Image Settings dialog\n\n 2. Click on the channel name to open a panel of sliders\n\n 3. Click on the  button next to any of the histogram values\n\n 4. Close the Image Settings dialog by clicking on the **X** button at the top right corner of the popup dialog\n\n\n This feature is only available for multispectral images.\n
\n\n\n\n
\n\nTo automatically configure the black and white points for a single channel
\n\n 1. From within the Viewer, click on the  button at the bottom left of the Viewer to reveal the Image Settings dialog\n\n 2. Click on the channel name to open a panel of sliders\n\n 3. Click on the **Auto Scale** button below the sliders\n\n 4. Close the Image Settings dialog by clicking on the **X** button at the top right corner of the popup dialog\n\n\n\n
\n\nTo automatically configure the black and white points for all channels
\n\n 1. From within the Viewer, click on the  button at the bottom left of the Viewer to reveal the Image Settings dialog\n\n 2. Click on the **Auto Scale** button at the bottom of the dialog\n\n 3. Close the Image Settings dialog by clicking on the **X** button at the top right corner of the popup dialog\n\n\n\n
\n","slug":"docs/viewer/image-settings"},{"frontmatter":{"title":"","description":null},"rawBody":"---\nredirect: /docs/viewer/overview/\n---\n","slug":"docs/viewer/"},{"frontmatter":{"title":"Overlays Panel","description":"overlays panel"},"rawBody":"---\ntitle: Overlays Panel\ndescription: overlays panel\norder: 21\nsection: Viewer\n---\n\n\n# Overlays Panel\n\nTo reset all black and white points to their default values
\n\n 1. From within the Viewer, click on the  button at the bottom left of the Viewer to reveal the Image Settings dialog\n\n 2. Click on the **Reset Scale** button at the bottom of the dialog\n\n 3. Close the Image Settings dialog by clicking on the **X** button at the top right corner of the popup dialog\n\n\n\nThe overlay feature allows one or more images to be attached to an image in the Repository. This feature has been designed for visualizing image analysis results such as segmentation results.\n\nWhen multiple overlays are attached to an image, the z-position of each overlay in the stack is determined by the position of the overlay in the Overlays panel. The first entry in the panel is visually on the bottom of the stack and subsequent entries are positioned higher in the stack. The image that overlays are attached to is positioned visually below all of the overlays.\n\n\n## Attaching Overlays\n\nOverlays are by default positioned at the top left corner of the image they have been attached to, at the base resolution layer. The initial height and width of the overlay will match the overlay's base resolution layer (i.e., pixel scaling of the overlay is not considered). An overlay image can be repositioned using the [Transform](#overlay-transform) properties.\n\n
\n Sub-images may complicate overlay positioning for the following reasons: 1) if the image has multiple sub-images, the overlay’s position is determined relative to the first sub-image, at the base resolution layer; and 2) if the overlay contains multiple sub-images, only the first sub-image is viewable.\n
\n\n
\n\nAttach an overlay using drag and drop
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. Upload an image from your computer by dragging a [supported image](/docs/overview/supported-formats/#supported-image-formats) file onto the sidebar\n\n\n\n
\n\n\n### Deleting Overlays\n\nOverlays can be deleted from the Overlays panel.\n\nAttach an overlay using the file selection dialog
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. Click on the **+** button at the top of the sidebar to reveal the **Add image overlay** dialog\n\n 3. Click in the blue box to activate the file selection dialog or simply drag an image into the blue box\n\n 4. Click on the **Start upload** button\n\n 5. Click on the **X** button at the top right of the popup dialog or anywhere outside of the dialog box to close it\n\n\n\n
\n\n\n## Overlay Properties\n\nTo delete an overlay from the Overlays panel
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. Identify the overlay entry to be modified\n\n 4. Click on the  button\n\n 5. Click on the **OK** button to confirm\n\n\n If you attempt to modify an item which is governed by a reason for change tracking policy, you will be required to provide a reason for the change.\n
\n\n
\n\n\n### Overlay Visibility\n\nOverlays are visible on the image by default once attached.\n\nTo rename an overlay from the Overlays panel
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. Identify the overlay entry to be modified\n\n 4. Click on the name of the entry\n\n 5. Provide a name or edit the existing text\n\n 6. Press the **Enter** key or click away from the textbox to save your changes\n\n\n\n
\n\nTo change the visibility of individual overlays
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. Identify the overlay entry to be modified\n\n 4. Click on the  button to toggle visibility\n\n\n\n
\n\n\n## Overlay Transform\n\nBy default, overlays are positioned at the origin (top left corner of the image's first sub-image's base resolution layer). If an uploaded overlay is meant to span a different region of interest, an appropriate transform may be defined.\n\nTo change the visibility of all overlays
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. Click on the  button at the top right corner of the Overlays panel to toggle visibility for all overlays\n\n\n\n
\n\n### Transform Limitations\n\nTransform operations may be limited for a given overlay depending on how it was generated.\n\n- Manually created overlays can be moved and resized\n- Overlays imported from [Indica Labs HALO](/docs/integrations/halo-integration/) cannot be moved or resized\n- [Visiopharm](/docs/integrations/visiopharm-integration/) MLD files converted to overlays can be moved, however the point of origin is the default position of the overlay and not the top left corner\n - These overlays can also be resized, but doing so may affect their position\n- Heatmap overlays imported from Visiopharm can be moved and resized.\n\n\n## Overlay Rendering\n\nOverlays have a number of properties that define how they are rendered. These properties are shared for all team members and therefore, changes made by any user will be visible to other users.\n\nTo reposition an overlay
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. Click on the  button next to an entry name in the panel to open the transform controls\n\n 4. Perform one of the following:\n 1. Set the X and Y values to specify the coordinates of the top left corner (with respect to the image) and set the W (width) and H (height) values to specify the extent of the overlay, or\n 2. Click on the  button to scale the overlay so that it fits the image width\n\n\n\n All values should be provided in pixel coordinates relative to the base resolution level of the image\n
\n\n\n\n
\n\nTo change the opacity of an overlay
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. Adjust the opacity slider in the range of [0, 100] for an entry in the Overlays panel\n\n\n\n
\n\nTo add pseudocolor to an overlay
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. Click on the **+ Add Pseudocolor** button for an entry in the Overlays panel\n\n 3. (Optional) Click on the color block to open the color palette and select a color from the palette\n\n\n\n
\n\nTo remove pseudocolor from an overlay
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. Click on the **x Remove** button next to the color block of an entry in the Overlays panel (only available if a pseudocolor has been previously defined)\n\n\n\n
\n\n\n### Compositing Operations\n\nVarious compositing techniques are available for rendering overlaid images. These are a number of other modes that may be helpful depending on the types of images and desired effects.\n\nTo change the composite operation for an overlay
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. Select a composite mode from the dropdown menu for an entry in the Overlays panel. See [compositing operations](#compositing-operations) for more details. The default composite operation is \"Normal\"\n\n\n\n
\n","slug":"docs/viewer/overlays"},{"frontmatter":{"title":"Image Information Panel","description":"image information panel"},"rawBody":"---\ntitle: Image Information Panel\ndescription: image information panel\norder: 17\nsection: Viewer\n---\n\n\n# Image Information Panel\n\nOverlay composition modes
\n\n | Composite mode | Description |\n | ----------------- | ------------- |\n | Normal | Draw this image on top of existing content. |\n | Source In | Draw this image only where it overlaps existing content. Non-overlapping areas are made transparent. |\n | Source Out | Draw this image only where it doesn’t overlap existing content. |\n | Source Atop | Draw this image only where it overlaps existing content. |\n | Destination Over | Draw this image behind existing content. |\n | Destination In | Draw existing content only where it overlaps this image. Non-overlapping areas are made transparent. |\n | Destination Out | Draw existing content only where it does not overlap this image. |\n | Destination Atop | Draw existing content only where it overlaps this image. This image is drawn behind existing content. |\n | Lighter | Add color values of this image with the color values of the existing content. |\n | Copy | Replace the existing content with this image. |\n | XOR | This image and existing content are drawn only where there is no overlap. |\n | Multiply | Multiply the color values of this image with the color values of existing content. |\n | Screen | Color values of this image and the existing content are inverted, multiplied, then inverted again. |\n | Overlay | A combination of multiply and screen. |\n | Hard Light | Like overlay, but with the top and bottom layers swapped. |\n | Soft Light | A softer version of hard light. |\n | Darken | Retain the darkest pixel between this image and the existing content. |\n | Color Dodge | Divide the color values of the existing content by the inverted color values of this image. |\n | Color Burn | Divide the inverted color values of the existing content by the color values of this image, and then invert the result. |\n | Difference | Subtract the color values of this image from the color values of the existing content and compute the absolute value. |\n | Exclusion | Like difference, but with lower contrast. |\n | Hue | Preserve the luma and chroma of the existing content while adopting the hue of this image. |\n | Saturation | Preserve the luma and hue of the existing content while adopting the chroma of this image. |\n | Color | Preserve the luma of the existing content while adopting the hue and chroma of this image. |\n | Luminosity | Preserve the hue and chroma of the existing content while adopting the luma of this image. |\n\n\n\nThe Image Information panel provides information about the currently open file. In this panel, you can find the slide label (if available) as well as any metadata fields, tags and snapshots associated with the file.\n\n
\n\n
\n\nTo toggle the visibility of the Image Information panel
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Click on the  button in the left sidebar to open the Image Information panel\n\n\n\n
\n\n\n## Image (Slide) Label\n\nIf a slide label is available, it will be displayed at the top of the Image Information panel.\n\nTo resize the Image Information panel
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. Click and drag the right border of the panel to resize it\n\n\n Slide label may contain PI and as such, the label is hidden for users that do not have the \"View Protected Information\" permission flag.\n
\n\n\n\n
\n\nTo view the slide label
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n\n\n
\n\n\n## Editing Image Tags\n\nAll the tags currently associated with the file will be listed in the \"Tag\" section of the Image Information panel.\n\nTo rotate the slide label
\n\n 1. Hover over the label with the mouse\n\n 2. Click on the  button until the desired orientation is achieved\n\n\n\n
\n\nTo add a tag
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. Click on the field showing the current tags (or **Add a tag...** if none have been added)\n\n 4. (Optional) Type a few letters to filter the list of tags\n\n 5. Select a tag from the dropdown menu\n\n 6. (Optional) To create a new tag, click on the **+ New tag** button after typing a new tag name\n\n\n\n
\n\n\n## Image Description\n\nA description can be added to an image which will be visible to all users.\n\nTo remove an existing tag
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. Click on the **X** button of the relevant tag\n\n\n\n \n\n
\n\n\n## Image Metadata and Fields\n\nAll of the metadata fields associated with the file are listed in the Image Information panel. You can click on a Custom Field metadata value to jump to a search using that criteria.\n\nTo edit image description
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. Click on the current description text (or **Add Description** if nothing has yet been written). This is directly below the tag section\n\n 4. Type a description of the image\n\n 5. Press **Enter** key or click anywhere else in the Viewer when done to save your changes\n\n\n\n If you attempt to modify an item which is governed by a reason for change tracking policy, you will be required to provide a reason for the change.\n
\n Metadata fields that are marked with \"May contain PI\" will be hidden (field value will be \"Anonymized\") for users that do not have the \"View Protected Information\" permission.\n
\n\n\n\n \n\n
\n\n\n## Downloading an Image\n\nTo edit image metadata
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. Click on the **Edit Metadata** button\n\n 4. (Optional) You can change the name of the image in the **Image Name** field\n\n 5. (Optional) Click on the **Add Fields** dropdown menu and select a field\n\n 6. (Optional) Change the value(s) of the listed field(s) accordingly, or clear the value by clicking on the gray **X** inside the field at the right-hand side\n\n 7. (Optional) Click on the red **X** button at the far right-hand side, outside of a field, to remove it from the item\n\n 8. Click on the **Update** button to save your changes, or click on the **X** button at the top right corner of the popup dialog to cancel\n\n\n\n If you attempt to modify an item which is governed by a reason for change tracking policy, you will be required to provide a reason for the change.\n
\n Only users with the \"Download File\" and \"Download Image\" permission flag are able to download files and images, respectively.\n
\n\n\n\n \n\n
\n\n\n## Deleting an Image\n\nTo download the image being viewed to your computer
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. Click on the image name\n\n 4. Click on **Download** in the dropdown menu\n\n 5. If prompted, select a location to save the downloaded file\n\n\n\n If the image is a multi-file image format the Download entry will be replaced with Download As. Hover over it to expand that menu, then select an archive file format in the expanded menu.\n
\n Only users with the \"Delete File\" permission flag are able to move images to the Trash.\n
\n\n \n\n
\n\n\n## Editing Snapshots\n\nAny [snapshot](/docs/viewer/snapshots/) associated with the current image will be listed in the Snapshots section of the Image Information panel.\n\nTo move the currently open and selected image to the Trash
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. Click on the image name\n\n 4. Click on **Send to Trash** in the dropdown menu\n\n 5. Click on the **Yes** button to confirm\n\n\n\n If you attempt to move an item which is governed by a reason for change tracking policy to Trash, you will be required to provide a reason for the change.\n
\n\n
\n\nTo navigate to the location of a snapshot in the Viewer
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. Scroll down to the **Snapshots** section\n\n 4. Select a snapshot by clicking on its thumbnail to reveal more options, then click on the **Open** button. Alternatively, you may double click on the thumbnail\n\n\n\n
\n\nTo download a snapshot as an image
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. Scroll down to the **Snapshots** section\n\n 4. Select a snapshot by clicking on its thumbnail to reveal more options, then click on the **Download** button\n\n 5. Adjust preferences\n 1. (Optional) Show/hide image annotations via the show annotations toggle\n 2. (Optional) Enable the show label toggle to reveal a text overlay\n 3. (Optional) Enable the show scale bar toggle to reveal a scale bar\n\n 6. Click on the **Download** menu\n\n 7. Adjust preferences such as\n - **Size**: adjust the width or height to specify the desired size\n - **File type**: select the desired format from the dropdown menu\n - **White Background**: Enable to use a white background instead of the default black\n\n 8. Click on the **Download** button\n\n 9. If prompted, select a location to save the downloaded file\n\n\n\n \n\n
\n\nTo rename a snapshot
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. Scroll down to the **Snapshots** section\n\n 4. Select a snapshot by clicking on its thumbnail to reveal more options, then click on the **Rename** button\n\n 5. Edit the name in the popup menu\n\n 6. Click on the **Rename** button\n\n\n\n If you attempt to modify an item which is governed by a reason for change tracking policy, you will be required to provide a reason for the change.\n
\n\n \n\n
\n","slug":"docs/viewer/information-panel"},{"frontmatter":{"title":"Overview Tool","description":"overview tool"},"rawBody":"---\ntitle: Overview Tool\ndescription: overview tool\norder: 16\nsection: Viewer\n---\n\n\n# Overview Tool\n\nTo delete a snapshot
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. Scroll down to the **Snapshots** section\n\n 4. Select a snapshot by clicking on its thumbnail to reveal more options, then click on the **Delete** button\n\n 5. In the popup dialog, click on the **Yes** button to confirm\n\n\n\n If you attempt to modify an item which is governed by a reason for change tracking policy, you will be required to provide a reason for the change.\n
\n\nThe Image overview provides a thumbnail of the image and contains an embedded indicator for the region of the image currently shown on the Viewer. The overview tool also displays an overlaid heatmap of all the regions viewed by the logged-in user at various scale factors.\n\n
\n\n
\n\n\nTo maximize the overview tool
\n\n 1. Hover or click on the image to reveal the  **Overview** button at the bottom right of the panel\n\n 2. Click on the  **Overview** button\n\n\n\n
\n\n\n### Current Region\n\nThe current region that is being displayed in the viewport is represented by the green rectangle on the image overview panel. You can also click on the overview to move the viewport to that location.\n\n\n## Heatmap\n\nThe heatmap automatically tracks all the regions viewed by the logged-in user. The resolution of the heatmap is limited to the resolution of the thumbnail image used in the overview tool.\n\nThe color retained by the heatmap in a given area is the highest magnification viewed at the location. The colors of the map represent the scale at which different regions have been viewed:\n\n- Blue ≥ 10%\n- Yellow ≥ 20%\n- Purple ≥ 40%\n- Light blue ≥ 60%\n- Green ≥ 80%\n- Red ≥ 98%\n\nTo minimize the overview tool
\n\n 1. Click on the  button to the top left of the overview tool\n\n\n\n
\n\nTo toggle the visibility of the heatmap
\n\n 1. Hover or click on the image to reveal the  **Overview** button at the bottom right of the panel\n\n 2. Click on the  **Overview** button\n\n 3. Click on the  button to the top left of the overview tool\n\n\n\n
\n","slug":"docs/viewer/overview-tool"},{"frontmatter":{"title":"Overview","description":"overview"},"rawBody":"---\ntitle: Overview\ndescription: overview\norder: 14\nsection: Viewer\n---\n\n\n# Overview\n\nTo reset the heatmap
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar to open the Help panel\n\n 3. Scroll down to the end of the panel and click on **Clear Heatmap**\n\n 4. Click on the **OK** button to confirm selection\n\n\n\nWhen you click on an image in a folder, PathcoreFlow will open the Viewer. The Viewer is optimized for viewing whole slide images and supports a range of [image formats](/docs/overview/supported-formats/#supported-image-formats) from many current and former scanner vendors. The Viewer provides a consistent set of tools and behaviors across all supported images. Generally speaking, the Viewer supports the following data types:\n\n- RGB (e.g., brightfield images)\n- Single channel grayscale\n- Multi-channel grayscale (e.g., multispectral, fluorescence, etc.)\n\n\n## Sub-images\n\nSome image files may contain multiple fields of view spanning a larger scan area (like a collage). These image files are more complex than traditional WSI because a file contains multiple images (a.k.a., sub-images), each of which may have different scanning properties.\n\nWhile the Viewer treats each file as a single image, it allows the user to configure some of the properties of sub-images independently (e.g., focal plane and render settings).\n\nIf an image file contains sub-images that are separated by empty space (i.e., areas that are not scanned), the background color is automatically chosen, often to match the approach in the image vendor's native viewer.\n\nThe Viewer seamlessly handles overlapping sub-images and allows the highest available magnification to be used across all sub-images.\n","slug":"docs/viewer/overview"},{"frontmatter":{"title":"Share Links Panel","description":"share links panel"},"rawBody":"---\ntitle: Share Links Panel\ndescription: share links panel\norder: 24\nsection: Viewer\n---\n\n\n# Share Links Panel\n\n
\n\nThe Share Links panel displays a list of all of the share links for the currently selected image in the Viewer, as well as tags describing the properties of each of those share links.\n\nSee the [Share Links](/docs/share-links/) section for more details on creating and managing share links.\n\n
\n\n
\n\nTo toggle the visibility of the Share Links panel
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Click on the  button in the left sidebar to open the Share Links panel\n\n\n\n
\n","slug":"docs/viewer/share-links-panel"},{"frontmatter":{"title":"Snapshots","description":"snapshots"},"rawBody":"---\ntitle: Snapshots\ndescription: snapshots\norder: 23\nsection: Viewer\n---\n\n\n# Snapshots\n\nTo resize the Share Links panel
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. Click and drag the right border of the panel to resize it\n\n\n\nSnapshots are designed for tracking and exporting regions of interest from images. The region of interest contained in a snapshot can be decorated with annotations, a label, and a scale bar prior to being exported as a PNG, JPEG, TIFF, or PDF file. These capabilities make it convenient to use snapshots, instead of image editing software, to prepare ROIs for publications or reports. For more advanced cases, where multiple images or ROIs are needed, consider using the [Figure Maker](/docs/viewer/figure-maker/).\n\n
\n Though snapshots are similar to rectangular annotations, they are distinct from geometric annotations, have different properties and are typically used for exporting annotated regions for reports.\n
\n\n\n## Creating Snapshots\n\nUse the snapshot tool to define a rectangular region of interest. The bounding box of a snapshot is recorded as metadata, making it visible from the [Image Information Panel](/docs/viewer/information-panel/) and from the Metadata tab in the [Folder Listing](/docs/repository/folder-listing/).\n\n\n\n
\n\nTo create a snapshot
\n\n 1. From within the Viewer, right-click on an image to open up the annotation ring\n\n 2. Select the  tool\n\n 3. Hold and drag the frame to capture a region of interest\n\n 4. (Optional) In the popup dialog, click on the first line of text (default: \"Untitled Snapshot\") and provide a name for the snapshot\n\n 5. (Optional) In the popup dialog, click on the second line of text (default: \"No description\") and provide a description for the snapshot\n\n\n\n The bounding box of a snapshot cannot be edited after it has been drawn.\n
\n\n\n\n
\n\n\n## Downloading Snapshots\n\nThe contents of a snapshot can be exported as a common image format (PNG, JPEG, TIFF, or PDF) for use in presentations or other documents. There are multiple locations where existing snapshots can be found and downloaded.\n\nTo navigate to an existing snapshot
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. Scroll down to the **Snapshots** section\n\n 4. Select a snapshot by clicking on its thumbnail to reveal more options, then click the **Open** button. Alternatively, you may double click on the thumbnail\n\n\n\n
\n\nTo download a snapshot from within the Viewer
\n\n 1. From within the Viewer, locate the snapshot on the image\n\n 2. Click on the snapshot title to reveal a dialog\n\n 3. Click on the **Download** button in the popup dialog\n\n 4. Adjust preferences\n 1. (Optional) Show/hide image annotations via the **Show annotations** toggle\n 2. (Optional) Enable the **Show label** toggle to reveal a text overlay\n 3. (Optional) Enable the **Show scale bar** toggle to reveal a scale bar\n\n 5. Click on the **Download** menu\n\n 6. Adjust preferences such as\n - **Size**: adjust the width or height to specify the desired size\n - **File type**: select the desired format from the dropdown menu\n - **White Background**: Enable to use a white background instead of the default black\n\n 7. Click on the **Download** button\n\n 8. If prompted, select a location to save the downloaded file\n\n\n\n
\n\n\n## Snapshot Markup\n\nWhen downloading a snapshot, certain markup tools can be used to annotate the region of interest prior to download. The markup settings are not saved and must be configured each time the snapshot download dialog is activated.\n\nTo download a snapshot from the Image Information panel
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. Scroll down to the **Snapshots** section\n\n 4. Select a snapshot by clicking on its thumbnail to reveal more options\n\n 5. Click on the **Download** button\n\n 6. Adjust preferences\n 1. (Optional) Show/hide image annotations via the **Show annotations** toggle\n 2. (Optional) Enable the **Show label** toggle to reveal a text overlay\n 3. (Optional) Enable the **Show scale bar** toggle to reveal a scale bar\n\n 7. Click on the **Download** menu\n\n 8. Adjust preferences such as\n - **Size**: adjust the width or height to specify the desired size\n - **File type**: select the desired format from the dropdown menu\n - **White Background**: Enable to use a white background instead of the default black\n\n 9. Click on the **Download** button\n\n 10. If prompted, select a location to save the downloaded file\n\n\n\n
\n\nTo include image annotations on a downloaded snapshot
\n\n 1. Enable the **Show annotations** toggle in the snapshot download dialog (all annotations visible on the image will be included)\n\n 2. To hide some annotations, ensure they are hidden prior to launching the download dialog\n\n\n\n
\n\nTo include a label on a downloaded snapshot
\n\n 1. Enable the **Show label** toggle in the snapshot download dialog\n\n 2. (Optional) Adjust the label text in the field below the toggle (default text will be the image name)\n\n 3. (Optional) Adjust the location of the label by clicking one of the four corners in the control to the left of **Alignment**\n\n 4. (Optional) Adjust the text color by clicking in the colored box to the left of **Foreground**, then selecting a color\n\n 5. (Optional) Adjust the text background color by clicking in the colored box to the left of **Background**, then selecting a color\n\n\n\n
\n\n\n## Snapshot Properties\n\nTo include a scale bar on a downloaded snapshot
\n\n 1. Enable the **Show scale bar** toggle in the snapshot download dialog\n\n 2. (Optional) Adjust the location of the scale bar by clicking one of the four corners in the control to the left of **Alignment**\n\n 3. (Optional) Adjust the text and scale bar color by clicking in the colored box to the left of **Foreground**, then selecting a color\n\n 4. (Optional) Adjust the **Show measurement text** toggle to show or hide the measurement\n\n 5. (Optional) Adjust the **Show border** toggle to show or hide a border around the text and scale bar\n\n 6. (Optional) Adjust the **Automatic length** toggle to determine the size of the scale bar\n - When enabled the size is determined automatically\n - When disabled the user can specify the size of the scale bar and select a unit of measurement from the dropdown menu\n\n 7. (Optional) Select the location of the measurement text relative to the scale bar from the **Text Alignment** dropdown menu (auto, left, center, or right)\n\n\n If you attempt to modify an item which is governed by a reason for change tracking policy, you will be required to provide a reason for the change.\n
\n\n
\n\nTo rename a snapshot from within the Viewer
\n\n 1. From within the Viewer, locate the snapshot on the image\n\n 2. Click on the snapshot title to reveal a dialog\n\n 3. Click on the first line of text in the popup dialog (default: \"Untitled Snapshot\")\n\n 4. Provide a name or edit the existing text\n\n 5. Press the **Enter** key or click away from the textbox to save your changes\n\n\n\n
\n\n\n### Snapshot Description\n\nThe description is a multiline text field that supports unicode characters. The description can be changed from within the Viewer. Enter new lines by pressing **Shift + Enter**.\n\nTo rename a snapshot from the Image Information panel
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. Scroll down to the **Snapshots** section\n\n 4. Select a snapshot by clicking on its thumbnail to reveal more options\n\n 5. Click on the **Rename** button\n\n 6. Provide a name or edit the existing text in the popup dialog\n\n 7. Click on the **Rename** button or press the **Enter** key to save your changes\n\n\n\n
\n\n\n### Snapshot Visibility\n\nSnapshots are visible on the image by default once created. If you need to declutter the image, you may hide all snapshots at once.\n\nTo change the description of a snapshot from within the Viewer
\n\n 1. From within the Viewer, locate the snapshot on the image\n\n 2. Click on the snapshot title to reveal a dialog\n\n 3. Click on the second line of text in the popup dialog (default: \"No description\")\n\n 4. Provide a description or edit the existing text\n\n 5. Press the **Enter** key or click away from the textbox to save your changes\n\n\n\n
\n\n\n## Deleting Snapshots\n\nSnapshots can be deleted from within the Viewer or from the Image Information panel.\n\nTo change the visibility of all snapshots
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. Scroll down to the **Snapshots** section\n\n 4. Click on the  button, adjacent to the **Snapshots** title, to toggle visibility for all snapshots\n\n\n\n
\n\nTo delete a snapshot from within the Viewer
\n\n 1. From within the Viewer, locate the snapshot on the image\n\n 2. Click on the snapshot title to reveal a dialog\n\n 3. Click on the **Download** button in the popup dialog\n\n 4. Click on the **OK** button to confirm\n\n\n\n
\n","slug":"docs/viewer/snapshots"},{"frontmatter":{"title":"Split View","description":"split view"},"rawBody":"---\ntitle: Split View\ndescription: split view\norder: 26\nsection: Viewer\n---\n\n\n# Split View\n##### \\[BioPharma] [Research+]\n\nSplit View allows multiple images to be opened simultaneously in the Viewer. Each image is confined to a dedicated panel within the viewing area and retains all the usual capabilities that are available when viewing a single image (e.g., annotating, panning, and zooming). Various layout options, such as side-by-side, vertical stacks, and 2-D grids, are available to aid the comparisons, as well as a range of functionality for image synchronization and panel management.\n\n\n## Viewing Multiple Images\n\nSplit View can be activated from various areas in the application; in general, wherever it is possible to select multiple images. Any tables that support right-click context menus will provide options for launching the Viewer with multiple images simultaneously. For instance, the [Folder Listing](/docs/repository/folder-listing/) table in the Repository, the [Search Results](/docs/search/search-overview/) table, and the Viewer's [Browse Folder Panel](/docs/viewer/browse-folder-panel/) can be used to select and view multiple images.\n\nTo delete a snapshot from the Image Information panel
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. Scroll down to the **Snapshots** section\n\n 4. Select a snapshot by clicking on its thumbnail to reveal more options\n\n 4. Click on the **Delete** button\n\n 5. Click on the **Yes** button to confirm\n\n\n Activating Split View from outside the Viewer will result in a 2-D grid layout with the most compact square dimensions for the number of images selected (e.g., 1x1, 2x2, 3x3, etc.). To have more control over image layout, activate Split View from the Viewer's Browse Folder Panel.\n
\n\n
\n To display the context menu on a mobile device, tap and hold on an item.\n
\n\n
\n\nTo launch Split View from the Repository
\n\n 1. Navigate to any folder in the Repository (click on the  **Repository** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu) then navigate to a folder)\n\n 2. Select one or more images by holding the **Ctrl** key (on Windows) or **⌘ / Command** key (on macOS) key and clicking on them\n\n 3. Bring up the context menu for the item (or items)\n\n 4. Click on **View Images**\n\n\n\n
\n\nTo launch Split View from Search
\n\n 1. Perform a search (click on the  **Search** button from the [Navigation Menu](/docs/repository/repository-overview/#navigation-menu) then execute a [basic query](/docs/search/search-overview/#basic-queries) or [advanced query](/docs/search/search-overview/#advanced-queries))\n\n 2. Select one or more images by holding the **Ctrl** key (on Windows) or **⌘ / Command** key (on macOS) key and clicking on them\n\n 3. Bring up the context menu for the item (or items)\n\n 4. Click on **View Images**\n\n\n\n \n\n
\n\nTo activate Split View from within the Viewer (by adding new images)
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. Select one or more images by holding the **Ctrl** key (on Windows) or **⌘ / Command** key (on macOS) key and clicking on them\n\n 4. Bring up the context menu for the item (or items)\n\n 5. Hover over **Add to View** in the dropdown menu to expand that menu\n\n 6. In the expanded menu, select the method for insertion into the existing layout\n - **Append as Row** inserts selection as a new row at the bottom of the layout\n - **Append to Bottom** inserts selection as new row(s) at the bottom of the layout, wrapping as required to maintain the grid width\n - **Append as Column** inserts selection as a new column at the right side of the layout\n - **Append to Right** inserts selection as new column(s) at the right side of the layout, wrapping as required to maintain the grid height\n\n\n\n Consider the Replace View option in step 5 if the selected images should replace the existing image(s) in the Viewer.\n
\n\n
\n\n\n## Panel Layout\n\nWhen viewing multiple images, the Viewer is divided into a 2-D grid with rows and columns. By default, the grid is regular and each panel (or cell) has the same size. The grid layout can be customized to create an irregular grid, where a panel can span multiple rows and/or columns. There are convenient options for creating three types of regular grids: side-by-side, vertically stacked, and 2-D grid.\n\nTo activate Split View from within the Viewer (by replacing existing images)
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. Select one or more images by holding the **Ctrl** key (on Windows) or **⌘ / Command** key (on macOS) key and clicking on them\n\n 4. Right-click on any of the selected images\n\n 5. Hover over **Replace View** in the dropdown menu to expand that menu\n\n 6. (Optional) Enable the **Randomize** toggle to add the images in a random order. Otherwise they are added in the order in which they were selected\n\n 7. In the expanded menu, select the desired method of replacing the images\n - **Grid** will arrange the images in the smallest possible square grid (e.g., 1x1, 2x2, 3x3, etc.)\n - **Side-by-side** will create a single row of images\n - **Stacked** will create a single column of images\n\n\n\n
\n\nTo change the number of rows or columns
\n\n 1. Click on the  button in the Viewer top bar to display the Layout dialog\n\n 2. From the **Rows** field, increase the number to append new rows to the bottom of the layout or decrease the number to remove empty rows from the layout\n\n 3. From the **Columns** field, increase the number to append new columns to the right of the layout or decrease the number to remove empty columns from the layout\n\n 4. (Optional) You can change the **Cell Aspect Ratio** between Fit, 16:9, 4:3, and 1:1\n\n 5. (Optional) You can adjust the **Grid Gap** slider to add more separation between the images\n\n\n\n
\n\nTo add an empty row
\n\n 1. Hover or click on any image adjacent to where you want to add the row, to reveal the toolbar at the top left of the panel\n\n 2. Click on the  button to expand the toolbar if necessary\n\n 3. Click on the  menu\n\n 4. From the dropdown menu, select **Insert Row Above** to add an empty row above the current image, or **Insert Row Below** to add an empty row below it\n\n\n\n
\n\nTo add an empty column
\n\n 1. Hover or click on any image adjacent to where you want to add the column, to reveal the toolbar at the top left of the panel\n\n 2. Click on the  button to expand the toolbar if necessary\n\n 3. Click on the  menu\n\n 4. From the dropdown menu, select **Insert Column Before** to add an empty column to the left of the current image, or **Insert Column After** to add an empty column to the right\n\n\n\n
\n\nTo remove any row or column from the layout
\n\n 1. Hover or click on any image from the row/column to be deleted, to reveal the toolbar at the top left of the panel\n\n 2. Click on the  button to expand the toolbar if necessary\n\n 3. Click on the  menu\n\n 4. Select **Remove Row** or **Remove Column** from the dropdown menu\n\n\n\n
\n\nTo move an image panel
\n\n 1. Hover or click on the image you want to move\n\n 2. Click on the  handle at the top right corner of the image and drag it to the new location\n\n\n\n
\n\n### Panel Aspect Ratio\n\nThe aspect of the ratio of the panels can be customized to any of the following values: 16:9, 4:3 and 1:1.\n\nTo create an irregular grid (by changing the span of panels)
\n\n 1. Hover or click on the image you want to span across multiple panels\n\n 2. Click on the  handle at the bottom right corner of the image and drag it to expand into panel(s) to the right and/or below the current panel\n\n\n\n \n\n
\n\n\n### Panel Spacing\n\nThe spacing between each panel (i.e., the separation between panels) can be customized.\n\nTo change the aspect ratio of panels
\n\n 1. Click on the  button in the Viewer top bar to display the Layout dialog\n\n 2. Click on the dropdown menu next to **Cell Aspect Ratio**\n\n 3. In the dropdown menu, select the desired aspect ratio\n - **Fit** will adapt the panels' size to attempt to fit all of them on the screen\n - **16:9** will enforce a 16:9 aspect ratio for the panels, even if scrolling is required to see all rows and/or columns\n - **4:3** will enforce a 4:3 aspect ratio for the panels, even if scrolling is required to see all rows and/or columns\n - **1:1** will force panels to remain square\n\n 4. (Optional) Enable the **Maximize Panels** toggle to expand all panels horizontally to fill the screen, rather than fitting the largest number of panels on screen at a time. This option is only available when aspect ratio is set to a value other than **Fit**\n\n\n\n Panel maximization can be used to control the width of panels. When Maximize Panels is enabled, panel widths are maximized such that the available width on the screen is fully utilized. As a result of the panel aspect ratio setting, panel maximization may reduce the number of panels that are visible on the screen at one time. When Maximize Panels is disabled, the width of panels are reduced (to a minimum size) to ensure the most number of panels are displayed on the screen at one time (without the need to scroll).\n
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\n\n\n## Panel Controls\n\nSplit View divides the available on-screen space for the image Viewer into one or more panels, depending on the number of images that have been chosen. While each panel can be independently controlled, only one panel can be controlled at any given point in time.\n\nTo change the spacing between panels
\n\n 1. Click on the  button in the Viewer top bar to display the Layout dialog\n\n 2. Adjust the **Grid Gap** slider to add space separating the panels\n\n\n The selected (controllable) image is denoted with a blue border around its panel and a blue dot adjacent to the file in the Browse Folder Panel of the Viewer. Images that appear in other panels are denoted with a gray dot in the Browse Folder panel.\n
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\n\nTo select an image for navigation
\n\n 1. Click into any panel to activate it. Note the blue border that appears around the active panel\n\n 2. Use the standard [Basic Controls](/docs/viewer/basic-controls/) to navigate the image\n\n\n\n
\n\nTo view the slide label for a panel
\n\n 1. Hover or click on the image to reveal the toolbar at the top left of the panel\n\n 2. Click on the  button to expand the toolbar if necessary\n\n 3. Hover over the  icon in the toolbar to see the slide label for that image\n\n\n\n
\n\nTo enable the rotation tool for the selected panel
\n\n 1. Hover or click on the image to reveal the toolbar at the top left of the panel\n\n 2. Click on the  button to expand the toolbar if necessary\n\n 3. Click on the  button in the toolbar to show or hide the rotation tool\n\n\n\n
\n\n### Color Management\n\nFor RGB images, the color correction profile of an image in a panel can be adjusted. The capabilities that are available in the Viewer are also available in Split View panels. See [Color Management](/docs/viewer/basic-controls/#color-management) for more details.\n\nTo add an image to an empty panel
\n\n 1. Click on the **Add an image** button in the center of an empty panel\n\n 2. In the **Select Cell Image** dialog that pops up, use either the Repository browser or Search to find the desired image\n\n 3. Click on the image to add it to the panel\n\n\n\n
\n\n\n## Panel Contents\n\nTo change the color management profile for the selected panel
\n\n 1. Hover or click on the image to reveal the toolbar at the top left of the panel\n\n 2. Click on the  button to expand the toolbar if necessary\n\n 3. Click on the  button in the toolbar to reveal the color management dialog\n\n 4. Select one of the available ICC color profiles\n\n\n\n
\n\nTo remove an image from a panel
\n\n 1. Hover or click on the image to reveal the toolbar at the top left of the panel\n\n 2. Click on the  button to expand the toolbar if necessary\n\n 3. Click on the  menu\n\n 4. Select **Remove Image** from the dropdown menu. This will leave an empty panel in its place\n\n\n\n
\n\n\n## Single Panel Mode\n\nActivating Split View reduces the screen area available for each image in the panel. If more screen area is required, it's possible to temporarily expand one panel to return to a single image configuration or to open any of any of panels in a new tab (in single panel mode).\n\nTo replace the image within a panel
\n\n 1. Hover or click on the image to reveal the toolbar at the top left of the panel\n\n 2. Click on the  button to expand the toolbar if necessary\n\n 3. Click on the  menu\n\n 4. Select **Change Image** from the dropdown menu\n\n 5. In the **Select Cell Image** dialog that pops up, use either the Repository browser or Search to find the desired image\n\n 6. Click on the image to add it to the panel\n\n\n\n
\n\nTo reset the Viewer to single image mode
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. Right-click on any image in the Browse Folder panel\n\n 4. Click on **Replace View** in the dropdown menu\n\n\n\n \n\n
\n\nTo open one image in a new tab (in single image mode)
\n\n 1. Hover or click on the image to reveal the toolbar at the top left of the panel\n\n 2. Click on the  button to expand the toolbar if necessary\n\n 3. Click on the  menu\n\n 4. Select **Open in Viewer** from the dropdown menu\n\n\n\n Any work performed in the new tab (e.g., new annotations created) will not be reflected in the original tab until a refresh (keyboard shortcut F5) is performed.\n
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\n\nTo expand a single image panel
\n\n 1. Hover or click on the image to reveal the toolbar at the top left of the panel\n\n 2. Click on the  button to expand the toolbar if necessary\n\n 3. Click on the  button\n\n\n\n
\n\nTo minimize an expanded panel (to return to Split View mode)
\n\n 1. Hover or click on the image to reveal the toolbar at the top left of the panel\n\n 2. Click on the  button to expand the toolbar if necessary\n\n 3. Click on the  button\n\n\n\n
\n\n\n## Synchronization\n\nImages can be synchronized so that panning and magnification actions are performed simultaneously on all images in the Viewer which have been marked as \"synchronized\".\n\nTo replace an image in the view with an image from the Browse Folder panel
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. Click and drag the desired image onto the panel containing the image to be replaced\n\n 4. In the **Replace Image** dialog that pops up, click on the **Yes** button\n\n\n\n
\n\nTo synchronize specific images
\n\n 1. Hover or click on the image to reveal the toolbar at the top left of the panel\n\n 2. Click on the  button\n\n 3. Repeat steps 1 and 2 for each image to synchronize\n\n\n\n
\n\nTo synchronize a row or column of images
\n\n 1. Hover or click on any image from the row/column to be synchronized, to reveal the toolbar at the top left of the panel\n\n 2. Click on the  button next to the  button\n\n 3. Select **Synchronize Row** or **Synchronize Column** from the dropdown menu\n\n\n\n
\n\n\n## Magnification\n\nThe magnification of the currently selected image can be applied to all synchronized images or to all images in the Viewer.\n\nIf you zoom an image that is part of a synchronized set, the change in magnification is also applied to other images in the set. When an image is pushed past its native resolution, the Viewer applies a [digital zoom](/docs/viewer/basic-controls/#digital-zoom).\n\nTo synchronize all images in the Viewer
\n\n 1. Click on the  button in the Viewer top bar to display the synchronize menu\n\n 2. Select **Synchronize All** from the dropdown menu\n\n\n When the digital zoom is applied as a result of zooming another image in the synchronized set, there is no restriction enforced. In this manner it is possible to attain a digital zoom greater than the 400% limit for a single image.\n
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\n\nTo apply the current magnification to all images in the Viewer
\n\n 1. Click on the current image magnification in the Viewer top bar\n\n 2. Select **Apply to All Slides** from the dropdown menu\n\n\n\n
\n\n\n## Drag and Drop\n\nFor convenience, images in the [Browse Folder Panel](/docs/viewer/browse-folder-panel/) can be dragged on to the Viewer, to either replace the images on display or to add new images to the Viewer.\n\nTo apply the current magnification to synchronized images
\n\n 1. Click on the current image magnification in the Viewer top bar\n\n 2. Select **Apply to Synchronized Slides** from the dropdown menu\n\n\n\n
\n\nTo replace a single image in Viewer using drag and drop
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. Click and drag a single image onto the panel containing the image to be replaced\n\n 4. In the **Replace Image** dialog that pops up, click on the **Yes** button\n\n\n\n
\n\nTo add multiple images to the Viewer using drag and drop
\n\n 1. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 2. Hover or click on the  button in the left sidebar\n\n 3. Select one or more images by holding the **Ctrl** key (on Windows) or **⌘ / Command** key (on macOS) key and clicking on them\n\n 4. Click and drag the images onto the panel containing the image to be replaced\n\n 5. In the **Placement** dialog that pops up, select **Add to View**\n\n 6. Select the method for insertion from the **Append** dropdown menu\n - **as Row** inserts selection as a new row at the bottom of the layout\n - **as Column** inserts selection as a new column at the right side of the layout\n - **to Bottom** inserts selection as new row(s) at the bottom of the layout, wrapping as required to maintain the grid width\n - **to Right** inserts selection as new column(s) at the right side of the layout, wrapping as required to maintain the grid height\n\n 7. (Optional) Enable the **Randomize** toggle to add the images in a random order. Otherwise they are added in the order in which they were selected\n\n 8. Click on the **Add Images** button\n\n\n\n
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