{"data":{"allMdx":{"nodes":[{"frontmatter":{"title":"Page not found","description":null},"rawBody":"---\ntitle: Page not found\n---\n\nimport { Box } from '@xstyled/styled-components'\nimport { Article, ScreenContainer, Button } from '../components'\nimport { Link } from \"gatsby\"\nimport notFoundImageURL from '../images/404.png'\n\n
\n \n \n There's a leak in the website.\n \n \n \n The page you are looking for does not actually exist.\n \n
\n \n
\n \n
\n","slug":"404"},{"frontmatter":{"title":"","description":null},"rawBody":"# FAQ page\n","slug":"faq"},{"frontmatter":{"title":"","description":null},"rawBody":"---\nslug: /docs\ntitle: \"\"\norder: 0\n---\n\n\n# PathcoreFlow\n\n## User Manual\n\n[Release Notes - v3.0](https://docs.pathcore.com/flow/release-notes/v3.0/)\n\n![PathcoreFlow Graphic](./images/flow-graphic.png)\n","slug":"docs/"},{"frontmatter":{"title":"","description":null},"rawBody":"---\nslug: /\nredirect: /docs/\n---\n","slug":""},{"frontmatter":{"title":"HALO Integration","description":"halo integration"},"rawBody":"---\ntitle: \"HALO Integration\"\ndescription: halo integration\nsection: Integrations\norder: 47\n---\n\n# HALO Integration\n##### \\[addon] \\[on-prem]\n\n
\n\nThe bi-directional integration between PathcoreFlow and the HALO image analysis software from Indica Labs provides capabilities for:\n\n- Using the HALO desktop application to perform image analysis on the images contained in the PathcoreFlow file repository (without downloading images to your PC)\n- Automatic recognition of analysis results generated in the HALO application in PathcoreFlow\n- Ability to view and share analysis results with colleagues from the PathcoreFlow environment\n\n
\n This integration requires the HALO desktop application to be installed on the PC from which the integration is to be used, and the HALO Integration addon for PathcoreFlow.\n
\n\n
\n\n
\n This integration is only available to customers that have an on-premise PathcoreFlow deployment. It is not available for cloud customers at this time.\n
\n\n\n## Integration Overview\n\nIn order to leverage the integration, image(s) must be launched from the PathcoreFlow environment using the **Open in Halo** context menu option. Doing so causes a SIS file to be downloaded. The SIS file is associated with the HALO application and when clicked will cause HALO — which is required to be installed on the user's PC — to launch with the selected image(s). At this stage in the workflow, PathcoreFlow only communicates metadata via the SIS file about the images that were selected for use in HALO.\n\n
\n The integration requires that PathcoreFlow and HALO be able to access the same network storage system and for PathcoreFlow to have access to HALO’s GraphQL server.\n
\n\nOnce the HALO app has launched, the user follows the normal workflow in that application and can proceed to interact with the HALO database and to perform analysis as they would normally.\n\nAnalysis results need not be exported since PathcoreFlow will query HALO’s GraphQL server for available results, as required, when users work with images in the PathcoreFlow environment. At present, PathcoreFlow can retrieve segmentation results, and any quantitative results (key-value pairs) an app may have generated. It’s important to note that these results will be automatically associated with the image(s) they were created from. These associations are made since PathcoreFlow and HALO are accessing the same underlying storage system and because the HALO application uses the file paths to identify images in its database.\n\nFinally, users are able to view images via any web browser, overlaid with any segmentation results that may have been found by PathcoreFlow. Thus the results and images are accessible from the PathcoreFlow environment and there is no duplication of data, since HALO and PathcoreFlow share the same underlying storage system.\n\n\n## Open in HALO From PathcoreFlow\n\nFrom the PathcoreFlow environment, one or more images and/or folders can be opened in HALO from the Repository page. Images can also be launched from within the Viewer, though this workflow is limited to the current image in the Viewer.\n\n
\n\n To launch HALO with a selection of images from the Repository \n\n 1. Navigate to any folder in the Repository (click on the ![Folder](./images/repository-folder.svg) **Repository** button from the left-hand sidebar 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. Right-click on the item (or items) to bring up the context menu\n\n 4. Click **Open in Halo**\n\n 5. A SIS file will be downloaded\n\n 6. Click on the downloaded SIS file to launch HALO\n\n
\n\n\n## Viewing Results in PathcoreFlow\n\nPathcoreFlow will automatically query HALO’s GraphQL server for the latest analysis results, as needed, when an image is opened in the Viewer or selected in the Repository page. If there is a need to refresh the results, simply refresh the browser by pressing the **F5** key or via the refresh button in PathcoreFlow.\n\n
\n\n To force PathcoreFlow to query HALO for the latest results \n\n 1. Navigate to any folder in the Repository (click on the ![Folder](./images/repository-folder.svg) **Repository** button from the left-hand sidebar then navigate to a folder)\n\n 2. Select an image that is out of sync\n\n 3. Click on the **Analysis Results** tab of the right-hand panel (or the bottom panel when viewing on a mobile device). You may need to click on the ![Collapsed](./images/sidebar-arrow-left.svg) button if the panel is collapsed\n\n 4. Click on the **Refresh** button at the bottom of the panel\n\n
\n\n\n### Viewing Segmentation Results\n\nSegmentation results retrieved from HALO are automatically associated with the correct image. As a result, entries are created for each result in the [Overlays Panel](/docs/viewer/overlays/) of the Viewer and these results are automatically overlaid and rendered on top of the image.\n\n
\n\n To see the segmentation results \n\n 1. Open the image in the PathcoreFlow Viewer\n\n 2. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 3. Hover or click on the ![Overlays](./images/layers.svg) button in the left sidebar\n\n 4. Look for entries following HALO's markup naming convention (e.g. \"\\_job47_MarkupActualTif.tif\" or \"20170418092916_job_132_analysis.tif\")\n\n
\n\nThe results behave similar to other overlays and their properties (e.g. opacity, render mode, and pseudocolor) can be manipulated. See [Overlays](/docs/viewer/overlays/) for more details.\n\n\n### Viewing Quantitative Results\n\nAny quantitative results exported to PathcoreFlow can be seen in multiple locations for convenience. When receiving these results, PathcoreFlow automatically creates a String [custom field](/docs/metadata/custom-fields/) for each key-value pair that is exported.\n\n
\n\n To view quantitative results from the Repository \n\n 1. Navigate to any folder in the Repository (click on the ![Folder](./images/repository-folder.svg) **Repository** button from the left-hand sidebar then navigate to a folder)\n\n 2. Select an image that has been processed with HALO\n\n 3. Click on the **Analysis Results** tab of the right-hand panel (or the bottom panel when viewing on a mobile device). You may need to click on the ![Collapsed](./images/sidebar-arrow-left.svg) button if the panel is collapsed\n\n 4. Look for the ![HALO](./images/halo.svg) icon next to the fields listed to identify results exported from HALO\n\n 5. Click on the ![Plus](./images/plus.svg) button to expand the quantitative results section\n\n
\n\n
\n\n To view quantitative results from within the Viewer \n\n 1. Open the image in the PathcoreFlow Viewer\n\n 2. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 3. Hover or click on the ![Info](./images/info.svg) button in the left sidebar\n\n 4. Look for the ![HALO](./images/halo.svg) icon next to entries in the list of overlays\n\n 5. Click on the ![Plus](./images/plus.svg) button to expand the quantitative results section\n\n
\n","slug":"docs/integrations/halo-integration"},{"frontmatter":{"title":"Visiopharm Integration","description":"visiopharm integration"},"rawBody":"---\ntitle: \"Visiopharm Integration\"\ndescription: visiopharm integration\nsection: Integrations\norder: 46\n---\n\n\n# Visiopharm Integration\n##### \\[addon] \\[on-prem]\n\n
\n\nThe bi-directional integration between PathcoreFlow and Visiopharm’s image analysis software provides capabilities for:\n\n- Using the Visiopharm desktop application to perform image analysis on the images contained in the PathcoreFlow Repository (without downloading images to your PC)\n- One click export of analysis results generated in the Visiopharm application to the PathcoreFlow Repository\n- Ability to view and share analysis results with colleagues from the PathcoreFlow environment\n- Ability to export annotations generated in PathcoreFlow to Visiopharm\n\n
\n This integration requires the Visiopharm desktop application to be installed on the PC from which the integration is used as well as the Visiopharm Integration addon.\n
\n\n\n## Integration Overview\n\nIn order to leverage the integration, image(s) must be launched from the PathcoreFlow environment using the **Open in VIS** context menu option. Doing so will launch the Visiopharm application — which is required to be installed on the user's PC — with the selected image(s). At this stage in the workflow, PathcoreFlow only communicates metadata about the images that were selected, enough for the Visiopharm application to locate these images.\n\n
\n The integration is coordinated via PathcoreFlow’s API and is therefore very efficient, transferring the least data possible and only as needed.\n
\n\nOnce the Visiopharm app has launched, the user follows the normal workflow in that application and can proceed to interact with the Visiopharm database and to perform analysis as they would normally. Other than the occasional prompt for your PathcoreFlow credentials, it will be largely transparent to the user that the images being processed in Visiopharm actually reside in the PathcoreFlow database securely over the network, rather than their own local storage.\n\nAs necessary, analysis results can be exported to the PathcoreFlow Repository via a dedicated export button in the Visiopharm application. At present, Visiopharm exports an MLD file which may contain segmentation results, overlays and/or heatmaps, as well as any quantitative results (key-value pairs) an app may have generated. It’s important to note that these results will be automatically associated with the image(s) they were created from. These associations can be made because the **Open in VIS** option was used to trigger the process in the first place.\n\nFinally, users are able to view images overlaid along with any MLD results that may have been exported in the PathcoreFlow environment via any web browser. Thus the results and images live in a single database and can be shared and retained easily via the PathcoreFlow Repository.\n\n\n## Open in Visiopharm From PathcoreFlow\n\nFrom the PathcoreFlow environment, one or more images and/or folders can be opened with Visiopharm from the Repository page. Images can also be launched from within the Viewer, though this workflow is limited to the current image in the Viewer.\n\n
\n\n To launch Visiopharm with a selection of images from the Repository \n\n 1. Navigate to any folder in the Repository (click on the ![Folder](./images/repository-folder.svg) **Repository** button from the left-hand sidebar 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. Right-click on the item (or items) to bring up the context menu\n\n 4. Click **Open in VIS**\n\n 5. (Optional) In the popup menu, select **Include annotations as ROI** to send PathcoreFlow annotations to Visiopharm\n\n 6. (Optional) In the popup menu, select **Map annotation colors to different ROI types** to to map the PathcoreFlow annotation colors to Visiopharm ROIs (this step may be needed for Visiopharm apps that rely on specified ROI labels)\n\n 7. Click on the **Open** button to launch Visiopharm\n\n
\n\n
\n\n To launch Visiopharm with all files in the current folder \n\n 1. Click on the ![Down Arrow](./images/repository-down-arrow.svg) button next to the current folder's breadcrumb\n\n 2. Click **Open in VIS**\n\n 3. (Optional) In the popup menu, select **Include annotations as ROI** to send PathcoreFlow annotations to Visiopharm\n\n 4. (Optional) In the popup menu, select **Map annotation colors to different ROI types** to to map the PathcoreFlow annotation colors to Visiopharm ROIs (this step may be needed for Visiopharm apps that rely on specified ROI labels)\n\n 5. Click on the **Open** button to launch Visiopharm\n\n
\n\n
\n\n
\n Your browser may warn that PathcoreFlow is opening an application. If so, you must allow this to happen in order for Visiopharm to launch. You may also make this preference permanent to avoid the extra step in the future.\n
\n\n\n## Exporting Results to PathcoreFlow\n\nUse the **Upload to PACS/IMS** button from the Visiopharm application to export the results that have been generated back to PathcoreFlow. This option may only be available for images that have been launched via the integration (i.e using the **Open in VIS** button) AND if your Visiopharm _Default Application_ preference in PathcoreFlow is set to “VIS” (as opposed to “VIS Basic” which is the default setting). See [My Account](/docs/settings/my-account/) to change preferences.\n\n
\n\n To export results for an image to PathcoreFlow from Visiopharm \n\n 1. Click on **File** to open File menu\n\n 2. Click on the **Save Data** button, or use the keyboard shortcut **Ctrl + S**, to save\n\n 3. Under **File** menu, choose **Export** from the left-hand sidebar\n\n 4. Click on the **Upload to PACS/IMS** button \\*\n\n\n \\* For convenience, the **Upload to PACS/IMS** button is also available from the Database panel in the Visiopharm application.\n\n
\n\nIf there are no errors in the Visiopharm application, export has happened successfully and the results should be visible in PathcoreFlow after several minutes. If multiple results are exported for the same image, PathcoreFlow will retain all of these results as well as the date/time they were exported.\n\nNewly received MLD files are immediately visible in the [Overlays Panel](/docs/viewer/overlays/) but they must be processed before their content becomes visible in the PathcoreFlow image Viewer. Refresh the page if you suspect a recent export from Visiopharm is not listed in the Overlays Panel.\n\n\n## Viewing Results in PathcoreFlow\n\nVisiopharm may export an MLD file, if available, and any quantitative results that have been generated by the app in the form of key-value pairs.\n\n\n### Viewing MLD Results\n\nMLD files exported from Visiopharm are automatically associated with the correct image. These results are recorded as entries in the Overlays Panel and the contents of the MLD files are automatically treated as an overlay and rendered on top of the image.\n\n
\n\n To see the MLD results \n\n 1. Open the image in the PathcoreFlow Viewer\n\n 2. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 3. Hover or click on the ![Overlays](./images/layers.svg) button in the left sidebar\n\n 4. Look for entries ending in **.mld** in the list of overlays\n\n
\n\nMLD results behave similar to other overlays and their properties (e.g. opacity, render mode, and pseudocolor) can be manipulated. See [Overlays](/docs/viewer/overlays/) for more details.\n\n
\n There may be multiple result sets exported from Visiopharm. Review the timestamp to differentiate these.\n
\n\n\n### Viewing Quantitative Results\n\nAny quantitative results exported to PathcoreFlow can be seen in multiple locations for convenience. When receiving these results, PathcoreFlow automatically creates a String [custom field](/docs/metadata/custom-fields/) for each key-value pair that is exported.\n\n
\n\n To view quantitative results from the Repository \n\n 1. Navigate to any folder in the Repository (click on the ![Folder](./images/repository-folder.svg) **Repository** button from the left-hand sidebar then navigate to a folder)\n\n 2. Select an image that has been processed with Visiopharm\n\n 3. Click on the **Analysis Results** tab of the right-hand panel (or the bottom panel when viewing on a mobile device). You may need to click on the ![Collapsed](./images/sidebar-arrow-left.svg) button if the panel is collapsed\n\n 4. Look for the ![Visiopharm](./images/vis.svg) icon next to the fields listed to identify results exported from Visiopharm\n\n
\n\n
\n\n To view quantitative results from within the Viewer \n\n 1. Open the image in the PathcoreFlow Viewer\n\n 2. If the left sidebar is not displayed, toggle it by clicking on the **Menu >** button at the bottom left of the Viewer\n\n 3. Hover or click on the ![Overlays](./images/layers.svg) button in the left sidebar\n\n 4. Look for an entry named “**LayerData.mld**” in the list of overlays\n\n 5. Click on the ![Plus](./images/plus.svg) button to expand the quantitative results section\n\n
\n","slug":"docs/integrations/visiopharm-integration"},{"frontmatter":{"title":"Bulk Import","description":"bulk import"},"rawBody":"---\ntitle: Bulk Import\ndescription: bulk import\norder: 9\nsection: Metadata\n---\n\n\n# Bulk Import\n##### [BioPharma]\n\n
\n\nMetadata fields can be imported from a CSV file in bulk. Values imported from CSV can be mapped to new or existing metadata fields and attached to any file in the Repository.\n\nWhen importing metadata from CSV, the entries in the first non-empty row will be treated as headers and the subsequent non-empty rows will be treated as metadata values. The values on each row will only be applied to a single file. The import process will attempt to identify the file in the Repository that matches each CSV row using the provided [File Naming Scheme](#file-naming-scheme). Once a file is matched to a row in the CSV, the selected values from the row will be attached to the file according to the field mapping defined.\n\n
\n\n To import metadata from a CSV file \n\n 1. Click on the ![Settings](./images/settings.svg) **Settings** button from the left-hand sidebar\n\n 2. Click on the **Fields** tab\n\n 3. Click on the **Import metadata** button\n\n 4. Click in the blue box to activate the CSV file selection dialog or simply drag a CSV file into the blue box\n\n 5. Define the **File Naming Scheme**. See [File Naming Scheme](#file-naming-scheme) for details\n\n 6. From the **Choose a Field** dropdowns, select or create a field that corresponds to each column of the CSV file (column names are shown adjacent to each dropdown)\n\n 7. Click on the **Preview Changes** button to see the results\n\n 8. Click **Commit Changes** if satisfied with the summary of results. Otherwise, click on **CSV Mapping** to reopen that section and adjust the import settings\n\n\n
\n Once the changes have been committed, they cannot be undone.\n
\n\n
\n\n\n## File Naming Scheme\n\nThe file naming scheme is used to associate rows of a CSV file with records in the repository. It takes the form of a pattern used to assemble a file name from fixed text and column data from the CSV file. The file name computed for each row is matched against those in the database. If a match is found, the specified metadata is applied to the record.\n\nThe first row of the CSV is assumed to be the header row and the remaining rows are assumed to be metadata that are imported. Headers that are enclosed in {} within the naming scheme are considered placeholders and are processed as defined above.\n\n
\n Use the green + button beside a field to add that header as a placeholder in the file naming scheme template.\n
\n\n\n### Example\n\n1. Assuming the layout of an imported CSV file is:\n\n | Study | Animal | Dose Group | Stain |\n | -------- | ------ | ---------- | ----- |\n | 2021-365 | Dog | 5 | H&E |\n | 2021-365 | Dog | 6 | H&E |\n\n2. And the File Naming Scheme is: `Image_{Study}_{Animal}_{Dose Group}.svs`\n\n3. The import process would match the rows in the CSV file to the following items in the Repository:\n - Image_2021-365_Dog_5.svs\n - Image_2021-365_Dog_6.svs\n","slug":"docs/metadata/bulk-import"},{"frontmatter":{"title":"Field Sets","description":"field sets"},"rawBody":"---\ntitle: Field Sets\ndescription: field sets\norder: 8\nsection: Metadata\n---\n\n\n# Field Sets\n##### [BioPharma]\n\n
\n\nField sets may be used to group one or more fields. When a field set is applied to a folder or a file, all the fields from the set are attached in the order defined in the field set. Field sets can be used to create templates for recurring studies and are convenient for tracking and associating multiple fields to a file or folder at once.\n\n\n## Creating Field Sets\n\nEnsure that the fields needed for the field set have already been created, see [Working With Custom Fields](/docs/metadata/custom-fields/#working-with-custom-fields).\n\n
\n\n To view existing field sets \n\n 1. Click on the ![Settings](./images/settings.svg) **Settings** button from the left-hand sidebar\n\n 2. Click on the **Field Sets** tab\n\n
\n\n
\n\n To create a new field set \n\n 1. Click on the ![Settings](./images/settings.svg) **Settings** button from the left-hand sidebar\n\n 2. Click on the **Field Sets** tab\n\n 3. Click on the **Create Field Set** button\n\n 4. Type in a name for the set in the **Field Set Name** area\n\n 5. Select from existing fields by using the **Add a field...** dropdown\n\n 6. Click on the **Save Field Set** button when finished\n\n
\n\n\n## Editing Field Sets\n\nField sets can be updated with new fields, and fields currently associated with the set can be removed.\n\n
\n Changes made to a field set will not be reflected in Repository items which have previously had said field set applied. Repository items will maintain their existing fields and values, in the order they were applied.\n
\n\n
\n\n To edit a field set \n\n 1. Click on the ![Settings](./images/settings.svg) **Settings** button from the left-hand sidebar\n\n 2. Click on the **Field Sets** tab\n\n 3. Select the field set to be edited\n\n 4. (Optional) Type in a new name for the set in the **Field Set Name** area\n\n 5. (Optional) Select from existing fields by using the **Add a field...** dropdown\n\n 6. (Optional) Move a field up and down by clicking on the ![Drag](./images/drag.svg) handle to the left of the field name and dragging it to the new position\n\n 7. (Optional) Remove a field from the set by clicking on the red **X** to the left of the field name\n\n 8. Click on the **Save Field Set** button when finished\n\n
\n\n\n## Duplicating Field Sets\n\nAn existing field set can be duplicated and then modified. This can save some time if you have multiple similar sets to prepare.\n\n
\n\n To duplicate a field set \n\n 1. Click on the ![Settings](./images/settings.svg) **Settings** button from the left-hand sidebar\n\n 2. Click on the **Field Sets** tab\n\n 3. Locate the field set to be duplicated\n\n 4. Click on the **Duplicate** button at the right of the row\n\n 5. (Optional) Type in a new name for the set in the **Field Set Name** area\n\n 6. (Optional) Select from existing fields by using the **Add a field...** dropdown\n\n 7. (Optional) Move a field up and down by clicking on the ![Drag](./images/drag.svg) handle to the left of the field name and dragging it to the new position\n\n 8. (Optional) Remove a field from the set by clicking on the red **X** to the left of the field name\n\n 9. Click on the **Save Field Set** button when finished\n\n
\n\n\n## Applying Field Sets\n\nWhen a field set is applied to a folder or a file, all the fields from the set are attached in the order defined in the field set.\n\n
\n\n To apply a field set to a file or folder \n\n 1. Navigate to any folder in the Repository (click on the ![Folder](./images/folder.svg) **Repository** button from the left-hand sidebar then navigate to a folder)\n\n 2. Select a single item in a folder\n\n 3. View fields in the **Metadata** tab of the right-hand panel (or the bottom panel when viewing on a mobile device). You may need to click on the ![Collapsed](./images/sidebar-arrow-left.svg) button if the panel is collapsed\n\n 4. Click on the **Edit Metadata** button\n\n 5. In the popup dialog, click on the **Add Fields** dropdown\n\n 6. (Optional) Begin typing to search for a field set by name\n\n 7. Select a field set from the dropdown\n\n 8. (Optional) Enter values for the newly added fields\n\n 9. 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\n## Deleting Field Sets\n\nDeleting field sets does not remove the associated fields or the values applied to files/folders. Please see [Deleting Custom Fields](/docs/metadata/custom-fields/#deleting-custom-fields) if you would like to remove the fields.\n\n
\n\n To delete a field set \n\n 1. Click on the ![Settings](./images/settings.svg) **Settings** button from the left-hand sidebar\n\n 2. Click on the **Field Sets** tab\n\n 3. Select the field set to be deleted\n\n 4. Click on the **Delete Field Set** button\n\n 5. Click on the **Yes** button to confirm\n\n
\n","slug":"docs/metadata/field-sets"},{"frontmatter":{"title":"Custom Fields","description":"custom fields"},"rawBody":"---\ntitle: Custom Fields\ndescription: custom fields\norder: 7\nsection: Metadata\n---\n\n\n# Custom Fields\n##### [BioPharma]\n\n
\n\nCustom Fields are key-value pairs that can be associated with files and folders in the Repository. Fields have properties that are convenient for tracking metadata, including:\n\n- compatibility with [search](/docs/search/search-overview/) functions\n- value types and input validators for enforcing correct data entry\n- a flag to indicate its value “may contain PHI” for downstream anonymization\n- can be grouped into [field sets](/docs/metadata/field-sets/) as template for recurring study types\n- user access to fields can be controlled via [permission flags](/docs/settings/permissions/#permission-flags)\n\nFields at the folder-level may be used to track general information about a particular case or study and fields at file-level may be used to track additional information (e.g. stain type of an image).\n\nSome fields are defined automatically by the system (aka. system fields) and others may be user defined (aka. custom fields). To learn more about fields and their properties, see [Working With Custom Fields](#working-with-custom-fields).\n\n
\n To be able to change the properties of custom fields, special permissions are required. See Permission Flags or contact your administrator for more information.\n
\n\n\n## Working With Custom Fields\n\nFields are key-value pairs that can be associated with items (e.g. files, folders) in the Repository. Fields can be added or removed from items and field values can be edited by users that have the Edit metadata permission, see [Permission Flags](/docs/settings/permissions/#permission-flags).\n\nClicking on a field 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 Metadata fields that are marked with “May contain PHI” will be hidden (field value will be “Anonymized”) for users that do not have “View Protected Health Information” permission.\n
\n\n\n### Working With Fields From Within the Repository\n\nFields associated with any item in the repository can be edited from within the Repository.\n\n
\n\n To view an item’s fields \n\n 1. Navigate to any folder in the Repository (click on the ![Folder](./images/folder.svg) **Repository** button from the left-hand sidebar then navigate to a folder)\n\n 2. Select a single item in a folder\n\n 3. View fields in the **Metadata** tab of the right-hand panel (or the bottom panel when viewing on a mobile device). You may need to click on the ![Collapsed](./images/sidebar-arrow-left.svg) button if the panel is collapsed\n\n
\n\n
\n\n To add fields to an item \n\n 1. Navigate to any folder in the Repository (click on the ![Folder](./images/folder.svg) **Repository** button from the left-hand sidebar then navigate to a folder)\n\n 2. Select a single item in a folder\n\n 3. View fields in the **Metadata** tab of the right-hand panel (or the bottom panel when viewing on a mobile device). You may need to click on the ![Collapsed](./images/sidebar-arrow-left.svg) button if the panel is collapsed\n\n 4. Click on the **Edit Metadata** button\n\n 5. In the popup dialog, click on the **Add Fields** dropdown\n\n 6. (Optional) Begin typing to search for a field by name\n\n 7. Select a field from the dropdown\n\n 8. Enter values for fields accordingly\n\n 9. 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
\n\n To edit an item’s fields \n\n 1. Navigate to any folder in the Repository (click on the ![Folder](./images/folder.svg) **Repository** button from the left-hand sidebar then navigate to a folder)\n\n 2. Select a single item in a folder\n\n 3. View fields in the **Metadata** tab of the right-hand panel (or the bottom panel when viewing on a mobile device). You may need to click on the ![Collapsed](./images/sidebar-arrow-left.svg) button if the panel is collapsed\n\n 4. Click on the **Edit Metadata** button\n\n 5. Change the value(s) of the listed field(s) accordingly, or clear the value by clicking on the grey **X** inside the field at the right hand side\n\n 6. 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
\n\n To delete fields from an item \n\n 1. Navigate to any folder in the Repository (click on the ![Folder](./images/folder.svg) **Repository** button from the left-hand sidebar then navigate to a folder)\n\n 2. Select a single item in a folder\n\n 3. View fields in the **Metadata** tab of the right-hand panel (or the bottom panel when viewing on a mobile device). You may need to click on the ![Collapsed](./images/sidebar-arrow-left.svg) button if the panel is collapsed\n\n 4. Click on the **Edit Metadata** button\n\n 5. Click on the red **X** button at the far right hand side, outside of a field, to remove it from the item\n\n 6. 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\n### Working With Fields From Within the Viewer\n\nFields associated with any item that is viewable in the Viewer can be edited from within the Viewer.\n\n
\n\n To view an item’s fields \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 ![Info](./images/info.svg) button in the left sidebar\n\n 3. System and custom fields are displayed. You may need to scroll down to see them all\n\n
\n\n
\n\n To add fields to an item \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 ![Info](./images/info.svg) button in the left sidebar\n\n 3. Click on the **Edit Metadata** button\n\n 4. In the popup dialog, click on the **Add Fields** dropdown\n\n 5. (Optional) Begin typing to search for a field by name\n\n 6. Select a field from the dropdown\n\n 7. Enter values for fields accordingly\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
\n\n To edit an item’s fields \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 ![Info](./images/info.svg) button in the left sidebar\n\n 3. Click on the **Edit Metadata** button\n\n 4. Change the value(s) of the listed field(s) accordingly, or clear the value by clicking on the grey **X** inside the field at the right hand side\n\n 5. 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\n
\n\n To delete fields from an item \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 ![Info](./images/info.svg) button in the left sidebar\n\n 3. Click on the **Edit Metadata** button\n\n 4. Click on the red **X** button at the far right hand side, outside of a field, to remove it from the item\n\n 5. 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\n## Custom Field Settings\n\nCustom fields can be used to define metadata for tracking study or case information. Fields have properties such as a name, type, input validators to enforce correct data entry, and a PHI flag that is used for anonymization.\n\n\n
\n Fields are accessible to users that have the appropriate permissions, see Permissions.\n
\n\n
\n\n To view existing fields \n\n 1. Click on the ![Settings](./images/settings.svg) **Settings** button from the left-hand sidebar\n\n 2. Click on the **Fields** tab\n\n
\n\n\n
\n\n To create a new field \n\n 1. Click on the ![Settings](./images/settings.svg) **Settings** button from the left-hand sidebar\n\n 2. Click on the **Fields** tab\n\n 3. Click on the **Create Field** button\n\n 4. Select a type of field from the **Type** dropdown. See [Field Types](#field-types) more information about types\n\n 5. Type in a name for the field in the **Name** area\n\n 6. (Optional) Select “Field may contain protected health information (PHI)” if the field may contain PHI. See [Fields With PHI](#fields-with-phi) for more information about anonymization\n\n 7. (Optional) Select the appropriate validators if applicable. See [Field Validators](#field-validators) for more information about data entry errors\n\n 8. (Optional) For Dropdown types, use the **+ Add option** button to define each option\n\n 9. Click on the **Create Field** button when finished\n\n
\n\n\n## Editing Custom Fields\n\nThe properties of existing fields can be edited so long as the changes do not invalidate existing values of the field. For instance:\n\n- The type of field should not be changed after it has been associated with an item\n- Options in a dropdown field should be removed cautiously after they have been associated with an item\n\n
\n\n To edit the properties of an existing field \n\n 1. Click on the ![Settings](./images/settings.svg) **Settings** button from the left-hand sidebar\n\n 2. Click on the **Fields** tab\n\n 3. Select the field to be edited\n\n 4. Make changes as desired\n\n 5. Click on the **Save Field** button when finished, or click on the **Close** button to discard the changes\n\n
\n\n\n## Deleting Custom Fields\n\n
\n Deleting a field that is in use will affect all items in the Repository with that field.\n
\n\n
\n\n To delete an existing field \n\n 1. Click on the ![Settings](./images/settings.svg) **Settings** button from the left-hand sidebar\n\n 2. Click on the **Fields** tab\n\n 3. Select the field to be deleted\n\n 4. Click on the **Delete Field** button\n\n 5. Click on the **Yes** button to confirm\n\n
\n\n\n## Fields With PHI\n\nFields that contain protected health information (PHI) or other sensitive information may be marked as such. If the PHI flag has been set/checked for a field, the application will replace the value of the field with \"Anonymized\" for users that do not have the correct permissions. See [Permission Flags](/docs/settings/permissions/#permission-flags) for more details.\n\n\n## Field Types\n\nAll fields, including System fields and Custom fields, have one of the following types:\n\n| Field Type | Description |\n| -------------- | ------------------------------------------------------------ |\n| Text | Single line text field. May be used for unstructured or structured data such as comments or barcodes. See [Field Validators](#field-validators) |\n| Numbers | Supports integer and floating-point numeric values |\n| Checkbox | Supports true/false values |\n| Dropdown | Holds a single value from a list of possible options |\n| Date | A date field with calendar support for data entry |\n| DateTime | A field that holds a date and time. The user can enter the value using a popup calendar tool |\n| User | A dropdown containing entries for all active users and users pending activation |\n\n\n## Field Validators\n\nField validators are used to enforce the correct entry of data by users. Users will not be allowed to enter data into fields that do not conform to the correct pattern, if a validator is defined. The following validators are available:\n\n| Field Type | Validators |\n| -------------- | ------------------------------------------------------------ |\n| Text | **Min Length**: the minimum number of characters allowed
**Max Length**: the maximum number of characters allowed
**Pattern**: a regular expression conforming to [JS Regex](https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions) standard |\n| Numbers | **Integer**: if selected, requires an integer value; otherwise, floating point values are considered valid
**Minimum**: the minimum value allowed
**Maximum**: the maximum value allowed |\n| Checkbox | n/a |\n| Dropdown | n/a |\n| Date | **Minimum**: the oldest value allowed
**Maximum**: the latest value allowed |\n| DateTime | **Minimum**: the oldest value allowed
**Maximum**: the latest value allowed |\n| User | n/a |\n\n
\n\n
\n Validators are not enforced through the API and they are not enforced when fields are imported from a CSV file.\n
\n","slug":"docs/metadata/custom-fields"},{"frontmatter":{"title":"System Fields","description":"system fields"},"rawBody":"---\ntitle: System Fields\ndescription: system fields\norder: 6\nsection: Metadata\n---\n\n\n# System Fields\n\n
\n\nSome fields are defined automatically by the system for all Repository items. However, the fields defined by the system vary based on the type of items in the Repository. The table below summarizes the fields that are automatically generated for each type of item in the Repository.\n\n
\n Not all system fields are searchable. Only system fields that are available for all items (e.g. Name, Created, Last Modified) can be used in search expressions and in table columns, see Search.\n
\n\n| Field Name | | Repository Item Types | |\n| ------------------------------------------------------------ | :-------: | :-------------------: | :----------: |\n| | **Image** | **Attachment** | **Folder/Other** |\n| Name
*the name of an item* | x | x | x |\n| Description
*a long text description of an item* | x | x | x |\n| Created
*datetime of creation* | x | x | x |\n| Size
*file size in bytes* | x | x | x |\n| Image Dimensions
*maximum image dimensions in pixels* | x | | |\n| Magnification
*highest magnification available in a whole slide image (if available)* | x | | |\n\n\n## Editing System Fields\n\nWith the exception of the Name field, System fields are read-only.\n\n
\n The Name field can only be edited by users with appropriate permissions, see Permissions.\n
\n\n
\n\n To edit the name of a file or folder \n\n 1. Navigate to any folder in the Repository (click on the ![Folder](./images/folder.svg) **Repository** button from the left-hand sidebar then navigate to a folder)\n\n 2. Right-click on the item to bring up the context menu\n\n 3. Click **Rename**\n\n 4. In the popup dialog, type a new name for the folder\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","slug":"docs/metadata/system-fields"},{"frontmatter":{"title":"Tags","description":"tags"},"rawBody":"---\ntitle: Tags\ndescription: tags\norder: 5\nsection: Metadata\n---\n\n\n# Tags\n\n
\n\nTags provide a mechanism to recall items from the Repository faster (e.g. tag images for an upcoming presentation or to collate interesting images). Each item in the repository can have more than one tag associated with it.\n\n
\n Tags are private to the user that created them and cannot be shared at this time.\n
\n\n
\n\n To tag a file or folder \n\n 1. Navigate to any folder in the Repository (click on the ![Folder](./images/folder.svg) **Repository** button from the left-hand sidebar then navigate to a folder)\n\n 2. Select a single item in a folder\n\n 3. Locate the **Add a tag..** dropdown in the **Metadata** tab of the right-hand panel (or the bottom panel when viewing on a mobile device). You may need to click on the ![Collapsed](./images/sidebar-arrow-left.svg) button if the panel is collapsed\n\n 4. Choose a tag from the **Add a tag..** dropdown. To create a new tag, type directly into the field and click on the **+ New tag** option\n\n
\n\n
\n\n To remove a tag from a file or folder \n\n 1. Navigate to any folder in the Repository (click on the ![Folder](./images/folder.svg) **Repository** button from the left-hand sidebar then navigate to a folder)\n\n 2. Select a single item in a folder\n\n 3. From the **Metadata** tab of the right-hand panel (or the bottom panel when viewing on a mobile device), click the **X** button beside the tag to be removed. You may need to click on the ![Collapsed](./images/sidebar-arrow-left.svg) button if the panel is collapsed\n\n
\n\n
\n\n To see all items with a given tag \n\n 1. In the left-hand sidebar under the **TAGS** section, click on the tag name, or\n\n 2. If the left-hand sidebar is collapsed, hover over the **TAGS** icon then click on the tag name in the popout panel\n\n 3. In the Tag view:\n - Tagged files are listed in the Files section\n - Tagged folders are listed in the Folders section\n\n
\n\n
\n\n To edit a tag's name \n\n 1. In the left-hand sidebar under the **TAGS** section, click on the tag name to navigate to the tag page\n\n 2. At the top of the page, adjacent to the tag's name, click on the **Edit** button\n\n 3. Edit the name in the textbox that appears\n\n 4. Click on the **Save** button to change the name, or click on the **Cancel** button to discard the changes\n\n
\n\n
\n\n To delete a tag \n\n 1. In the left-hand sidebar under the **TAGS** section, click on the tag name to navigate to the tag page\n\n 2. Click on the **Delete Tag** button\n\n 3. Confirm to delete the tag and dissociate it from all Repository items\n\n
\n","slug":"docs/metadata/tags"},{"frontmatter":{"title":"Auxiliary Information","description":"auxiliary information"},"rawBody":"---\ntitle: Auxiliary Information\ndescription: auxiliary information\nsection: Report Templates\norder: 36\n---\n\n# Auxiliary Information\n\n## Report styles\n\nThe report template in PathcoreFlow uses Cascading Style Sheets or CSS to style the generated reports. More information about the supported CSS specifications can be found here:\n\n[https://doc.courtbouillon.org/weasyprint/stable/api_reference.html#css.](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```\n\n/* Define your CSS styles here */\n\n.container {\nfont-family: sans-serif;\n}\n\n.signature {\nmax-width: 3in;\ntext-align: center;\n}\n\n.signature img {\nmax-width: 100%;\n}\n\nimg {\nborder-style: solid;\n}\n```\n\n## Static data\n\nPredefined data can be added to a report in a flexible way by using the Static Data tab. Data entered there can be accessed inside the template as the variable static_data. The data is specified using the JavaScript Object Notation (JSON) format. See the link below for an introduction to the JSON format: [https://www.w3schools.com/js/js_json_syntax.asp](https://www.w3schools.com/js/js_json_syntax.asp).\n\n### Static Data Example\n\nThis section shows the report template code to display output from static_data.\n\n```\n

\nStatic Data\n

\n\n\n```\n\nThis section shows the Static Data values in JSON format.\n\n```\n{\n\"todo\": [\n\"define\",\n\"your\",\n\"static\",\n\"data\",\n\"here\"\n],\n\"name\": \"value\",\n\"date\": \"2020-08-18\"\n}\n```\n\n## Snapshots\n\nSnapshots can be displayed alongside their associated image or on their own within a report. If the desire is to only display snapshots, a snapshot container needs to be created within the Report Template. A snapshot container is an array of selected snapshots from the report folder.\n\n1. On the Snapshots tab under Report Template, click **Add Snapshot Container**\n\n2. Enter a Display Name for the snapshot container.\n3. Enter a Template Name.\\*\n4. Set the **Required** toggle if the report must contain snapshots\n5. Set between to the range of snapshots allowed/required in the report. (i.e. to force the user to select up to 5 snapshots to be included in the report, set between to 1 and 5)\n\n\\*This is the name of the snapshots container used inside the report template. That is, if you name the container selected_features, the list of snapshots can be accessed as the variable snapshots.selected_features.\n\n### Snapshots Example\n\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\n
\n\n{% endfor %}\n\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# Jinja2 Quick Reference\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](https://jinja.palletsprojects.com/en/3.0.x/templates/) documentation.\n\nNote: As the template engine is very flexible, the configuration from the [Pathcore] 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## 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## Variables\n\nVariables may have attributes or elements on them you can access, see the [Placeholder Reference].\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 double-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## 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 (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 `(str.join(', ', listx))`.\n\nFor more information about the builtin filters, see [https://jinja.palletsprojects.com/en/2.9.x/templates/#builtin-filters](https://jinja.palletsprojects.com/en/2.9.x/templates/#builtin-filters)\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\nFor more information about the builtin tests, see [https://jinja.palletsprojects.com/en/2.9.x/templates/#builtin-tests](https://jinja.palletsprojects.com/en/2.9.x/templates/#builtin-tests)\n\n## Comments\n\nTo comment-out part of a line in a template, use the comment syntax which is by default set to {# ... #}. 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\n{# note: commented-out template because we no longer use this\n{% for user in users %}\n...\n{% endfor %}\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. With the default syntax, 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```\n

Images

\n\n```\n\nAs variables in templates retain their object properties, it is possible to iterate over containers like dict:\n\n```\n
\n{% for key, value in folder.fields.items() %}\n
{{ key|e }}
\n
{{ value|e }}
\n{% endfor %}\n
\n```\n\nNote: e in `{{ key|e }}` is an alias for the builtin filter escape(s). The filter escape converts the characters &, <, >, ‘, and ” in string s to HTML-safe sequences. Use this if you need to display text that might contain such characters in HTML. Marks return value as markup string.\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 image in folder.images if not image.name == 'test' %}\n
  • {{ user.username|e }}
    • \n{% endfor %}\n```\n\nIf no iteration took place because the sequence was empty or the filtering removed all the items from the sequence, you can render a default block by using else:\n\n```\n\n```\n\n### If\n\nIn the simplest form, you can use the If statement to test if a variable is defined, not empty and not false:\n\n```\n{% if report_signed_by %}\n\n
    \n\n

    Signed by {{ report_signed_by.name }} at {{ report_signed_at }}

    \n
    \n\n{% endif %}\n```\n","slug":"docs/report-templates/jinja2-quick-reference"},{"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\nThe following is a larger report template example that illustrates various features including:\n\n| **Feature Example** | **Syntax** |\n| ------------------------------------------------- | ----------------------------------------------------------- |\n| Displaying variables | `{{ [folder.name](http://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['todo'] %}` |\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| Displaying image regions | `` |\n\n```\n{% block title %}\n {# Set the title of your PDF document in this block (text only) #}\n PDF Report Title\n{% endblock %}\n{% block body %}\n
    \n {# Add any text such as a report title or description of the report anywhere in the report template using different HTML blocks such as paragraph tags

    , line breaks
    , headings

    /

    / etc. #}\n

    Untitled Report

    \n

    Set the content of your report within the \"body\" block.

    \n

    \n Use variables passed to the template like this: The name of the case is {{ case.name }}.\n See the template designer documentation linked above for all the available features.\n

    \n

    \n Folder Name\n

    \n {# Displays the currently selected folder's name #}\n {{ folder.name }}\n

    \n Folder ID\n

    \n {# Displays the currently selected folder's ID in PathcoreFlow #}\n {{ folder.id }}\n

    \n Folder Description\n

    \n {# Displays the currently selected folder's description #}\n {{ folder.description }}\n

    \n Custom Fields\n

    \n {# Displays all the custom fields associated with the folder #}\n {{ folder.fields }}\n\n

    \n Static Data\n

    \n \n\n

    Images

    \n \n\n

    Attachments

    \n \n\n {# Snapshots can also be displayed without accessing their associated image #}\n

    \n Snapshots\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
    \n {% endfor %}\n\n\n

    If the report is signed, the signer's signature and name will appear here:

    \n {% if report_signed_by %}\n
    \n \n

    Signed by {{ report_signed_by.name }} at {{ report_signed_at }}

    \n
    \n {% endif %}\n
    \n{% endblock %}\n\n```\n","slug":"docs/report-templates/detailed-template-example"},{"frontmatter":{"title":"Placeholder Reference","description":"placeholder reference"},"rawBody":"---\ntitle: Placeholder Reference\ndescription: placeholder reference\nsection: Report Templates\norder: 35\n---\n\n# Placeholder Reference\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## 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## 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 by specifying its name. |\n| template_file_by_id(id) | Get a URL to the file contents of a Report Template File by specifying its id. |\n\n_Params_\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## Data Types\n\nSome commonly used properties for folders, images, attachments and snapshots are listed.\n\nNote: Some properties are omitted for brevity. The pprint filter in Jinja is useful for exploring the available properties in each variable.\n\n### Folder properties\n\n| **Name** | **Type** | **Description** |\n| ----------- | ------------ | --------------------------------------------------------------- |\n| id | int | The ID of this folder. |\n| name | string | The name of the folder. |\n| description | string | The description of the folder. |\n| attachments | Attachment[] | A list of attachments in this folder (i.e. non-image files). |\n| images | Image[] | A list of images in this folder. |\n| fields | dict | A dictionary mapping custom field names to custom field values. |\n\n### Attachment properties\n\n| **Name** | **Type** | **Description** |\n| -------- | -------- | ------------------------------------------ |\n| id | string | The ID of this file. |\n| name | string | The name of this file. |\n| file_url | string | A URL to access the contents of this file. |\n| filesize | int | The size of this file in bytes. |\n\n### Image properties\n\n| **Name** | **Type** | **Description** |\n| ------------------------ | -------- | ------------------------------------------------ |\n| id | string | The ID of this image. |\n| name | string | The name of this image. |\n| filesize | int | The size of this image in bytes. |\n| get_thumbnail(bounds) | function | Get a URL to access the thumbnail of this image. |\n| get_region(area, bounds) | function | Get a URL to access a region from this image. |\n\n_Params_\n\n| **Name** | **Type** | **Description** |\n| -------- | -------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |\n| area | int[] | A region to extract from the image specified as [x, y, width, height] in pixel coordinates of the original image. If omitted or invalid, the requested image is omitted from the report. |\n| bounds | int[] | A [width, height] pair in pixels that this image will be resized to fit within (if larger). If omitted, the requested image is returned unscaled and if invalid, the requested image is omitted from the report. |\n\n### Snapshot properties\n\n| **Name** | Type | **Description** |\n| ----------- | -------- | ------------------------------------------------- |\n| id | int | The ID of this snapshot. |\n| title | string | The title of this snapshot. |\n| description | string | The description of this snapshot. |\n| bounds | function | Get a URL to access this snapshot’s region image. |\n\n_Params_\n\n| **Name** | **Type** | **Description** |\n| --------- | -------- | -------------------------------------------------- |\n| name | string | The name of the user that signed the report. |\n| signature | string | A URL to the signature image of the report signer. |\n","slug":"docs/report-templates/placeholder-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# Report Templates Overview [addon]\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 arching and/or sharing study information in standard formats. Different report templates can be used for different studies, depending on the need.\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 within templates for populating 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] and [Placeholder Reference]. For comprehensive information about templating language, refer to documentation of the [Jinja2](https://jinja.palletsprojects.com/en/3.0.x/templates/) templating language.\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], [Placeholder Reference] and [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

    Basic Report Template

    \n

    Set the content of your report within the \"body\" block.

    \n

    Use variables passed to the template like this:

    \n

    The name of the folder is {{ folder.name }}.

    \n

    List of Images

    \n \n
    \n{% endblock %}\n```\n","slug":"docs/report-templates/report-templates-overview"},{"frontmatter":{"title":"Working With Reports","description":"working with reports"},"rawBody":"---\ntitle: Working With Reports\ndescription: working with reports\nsection: Report Templates\norder: 33\n---\n\n# Working With Reports\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\nNote: To be able to generate reports, users require Folder->View and File->Upload permissions and to be able to navigate to a folder and change its contents. In addition, to be able to view any generated report, the Files->View permission is required and to view images that may be linked into a report, users require the Images->View permission.\n\n
    \n\n To generate a report from an existing template \n\n1. Navigate to any folder in the Repository. (If not in a folder, click on the  ![Folder](./images/folder.svg)  button from the left-hand sidebar then choose a folder)\n\n2. Click **Generate Report\\***\n\n3. Enter a name in the **Report Name** field\n\n4. Select a Report Template from the drop down list\n\n5. (optionally) Toggle **Sign Report** to enabled in order to insert your signature in the report. To add a signature, see [Use Profile]\n\n6. (optionally) click **Preview**\n\n7. Click **Generate Report** 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 deployment.\n\n## Managing report templates\n\nTo better understand the features of the templating language, start by reviewing our [Jinja2 Quick Reference] and [Placeholder Reference]. For comprehensive information about templating language, refer to documentation of the [Jinja2](https://jinja.palletsprojects.com/en/3.0.x/templates/) templating language\n\nNote: The “Manage report templates” permission flag is required to create or edit report templates.\n\n
    \n\n To create a report template \n\n1. Click on the  ![Setting](./images/setting.svg)  button from the left-hand sidebar\n\n2. Click on the **Report Templates** tab\\*\n\n3. Click the **New Report Template** button\n\n4. Adjust the report template\n\n a. Type a name in the name field\n\n b. Adjust contents of the **Template** tab, see [Jinja2 Quick Reference] and [Placeholder Reference] for details\n\n c. (Optionally) Adjust content of the **Style**, **Static** and **Snapshots** tabs, see [Auxiliary Information] for details\n\n5. To preview the report template\n\n a. Click **Select Folder** from the top-right hand corner and choose a folder for testing\n\n b. (Optionally) Toggle **Signed** to include a signature\n\n c. Click the **Generate Preview** button to see the results\n\n6. Click **Save**\n\n
    \n\n
    \n\n To edit a report template \n\n1. Click on the  ![Setting](./images/setting.svg)  button from the left-hand sidebar\n\n2. Select the **Report Templates** tab\\*\n\n3. From the list of templates, click on the name of an existing template to open it OR click the on a row in the table and then click the **Edit** button\n\n a. (Optionally) Edit the name template in the textbox at the top of the page\n\n b. (Optionally) Adjust contents of the **Template** tab, see [Jinja2 Quick Reference] and [Placeholder Reference] for details\n\n c. (Optionally) Adjust content of the **Style**, **Static** and **Snapshots** tabs, see [Auxiliary Information] for details\n\n4. To preview the changes\n\n a. Click **Select Folder** from the top-right hand corner and choose a folder for testing\n\n b. (Optionally) Toggle **Signed** to include a signature in the preview\n\n c. Click the **Generate Preview** button to see the results\n\n5. Click **Save**\n\n
    \n\n
    \n\n To preview a report template \n\n1. Click on the  ![Setting](./images/setting.svg)  button from the left-hand sidebar\n\n2. Click on the **Report Templates** tab\\*\n\n3. From the list of templates, click on the name of an existing template to open it OR click the on a row in the table and then click the **Edit** button\n\n4. To preview the changes\n\n5. Click **Select Folder** from the top-right hand corner and choose a folder for testing\n\n6. (Optionally) Toggle **Signed** to include a signature in the preview\n\n7. Click the **Generate Preview** button to see the results\n\n
    \n\n
    \n\n To enable or disable a report template \n\n1. Click on the  ![Setting](./images/setting.svg)  **Settings** button from the left-hand sidebar\n\n2. Select **Report Templates** tab\\*\n\n3. Click the toggle beside the report to disable\n\n
    \n\n\\*The user-level Manage report templates permission is required for editing report templates. In addition, the reporting tools add-on is required for reporting functionality.\n","slug":"docs/report-templates/working-with-reports"},{"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\nNavigating through the folders in the Repository is similar to other file systems. Simply click into a folder to open it (i.e. enter into it) or click on a file to launch it. Any of the [supported image formats](/docs/repository/supported-formats/#supported-image-formats), such as whole slide images, DICOM images and photos, can be viewed with the built-in image viewer on-demand via streaming technologies. Many non-image data files will need to be downloaded and viewed using external software.\n\n
    \n\n To navigate to a folder \n\n 1. Click on the ![Folder](./images/folder.svg) **Repository** button from the left-hand sidebar\n\n 2. Navigate to a folder using the folders listing\n\n
    \n\n
    \n\n To create a new folder \n\n 1. Click on the ![Actions](./images/block-add.svg) 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\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\n
    \n You can navigate to the parent folder by clicking into the breadcrumb.\n
    \n\n\n### Current Folder Operations\n\nBy clicking the ![Down Arrow](./images/down-arrow-light.svg) 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 addons some operations may not be available.\n
    \n\n
    \n\n Move \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 ![Down Arrow](./images/down-arrow-light.svg) 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
    \n\n Copy \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 ![Down Arrow](./images/down-arrow-light.svg) 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
    \n\n Rename \n\n **Rename** allows you to change the name of the current folder.\n\n 1. Click on the ![Down Arrow](./images/down-arrow-light.svg) 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
    \n\n Edit Metadata \n\n **Edit Metadata** opens a dialog where you can add, change, or remove [Metadata](/docs/metadata/tags/) fields for the current folder.\n\n 1. Click on the ![Down Arrow](./images/down-arrow-light.svg) 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/). See the [Metadata](/docs/metadata/tags/) section for more details\n\n
    \n\n
    \n\n Share \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
    \n A Share icon in the breadcrumb indicates share links are associated with the current folder.\n
    \n\n 1. Click on the ![Down Arrow](./images/down-arrow-light.svg) 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. See [Managing Share Links](/docs/share-links/managing-share-links/) for more details\n\n
    \n\n
    \n\n Favorite / 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 See [Favorite Status](/docs/repository/repository-operations/#favorite-status) for more details.\n\n 1. Click on the ![Down Arrow](./images/down-arrow-light.svg) 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\n Download \n\n **Download** opens the [Download](/docs/repository/repository-operations/#downloading) dialog, allowing you to save the contents and metadata locally.\n\n 1. Click on the ![Down Arrow](./images/down-arrow-light.svg) 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). See [Downloading](/docs/repository/repository-operations/#downloading) for more details\n\n 4. Click on the **Download** button\n\n
    \n\n
    \n\n Open in VIS [addon] \n\n **Open in VIS** allows you to open the current folder in Visiopharm.\n\n 1. Click on the ![Down Arrow](./images/down-arrow-light.svg) 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. See [Visiopharm Integration](/docs/integrations/visiopharm-integration/) for more details\n\n 4. Click on the **Open** button\n\n
    \n\n
    \n\n Open in HALO [addon] \n\n **Open in HALO** allows you to open the current folder in Indica Labs's HALO software.\n\n 1. Click on the ![Down Arrow](./images/down-arrow-light.svg) 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. See [HALO Integration](/docs/integrations/halo-integration/) for more details\n\n
    \n\n
    \n\n Audit [addon] \n\n **Audit** opens the Audit Report dialog, which can generate a CSV file of changes made to the folder over a specified period of time.\n\n 1. Click on the ![Down Arrow](./images/down-arrow-light.svg) button next to the current folder's breadcrumb\n\n 2. Click **Audit**\n\n 3. In the popup dialog, select the start date from which you wish to see the audit data\n\n 4. Click on the **Download Audit** button to download a CSV file\n\n
    \n\n
    \n\n Delete \n\n **Delete** allows you to remove the folder and all of its contents from the Repository.\n\n
    \n Deleted items cannot be recovered. Be careful with this action.\n
    \n\n 1. Click on the ![Down Arrow](./images/down-arrow-light.svg) button next to the current folder's breadcrumb\n\n 2. Click **Delete**\n\n 3. Click on the **Yes** 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## Image Labels\n\nImage labels (sometimes called slide labels) can be shown in the Repository folder listing alongside an image's preview.\n\n
    \n\n To toggle image labels \n\n 1. Navigate to any folder in the Repository (click on the ![Folder](./images/folder.svg) **Repository** button from the left-hand sidebar then navigate to a folder)\n\n 2. Click on the ![Display Settings](./images/settings.svg) 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## 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\n
    \n\n To enable List View \n\n 1. Navigate to any folder in the Repository (click on the ![Folder](./images/folder.svg) **Repository** button from the left-hand sidebar 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 (![List](./images/display-list.svg)), Compact List (![Compact List](./images/display-compact.svg)), or Icon (![Icon](./images/display-icon.svg))\n\n 3. In the popup menu, click **List**\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\n
    \n The table columns and sort order are automatically remembered.\n
    \n\n
    \n\n To sort items in List View \n\n 1. Navigate to any folder in the Repository (click on the ![Folder](./images/folder.svg) **Repository** button from the left-hand sidebar 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 ![Up Arrow](./images/sort-up-arrow.svg) for ascending order and ![Down Arrow](./images/sort-down-arrow.svg) for descending order in the table header adjacent to the selected column)\n\n
    \n\n
    \n\n To add a column \n\n 1. Navigate to any folder in the Repository (click on the ![Folder](./images/folder.svg) **Repository** button from the left-hand sidebar then navigate to a folder)\n\n 2. Click on the ![Display Settings](./images/settings.svg) 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 ![Add Circle](./images/add_circle_18dp.svg) button next to a field in the **Available Columns** section\n\n 5. Click on the **Save** button\n\n
    \n\n
    \n\n To remove a column \n\n 1. Navigate to any folder in the Repository (click on the ![Folder](./images/folder.svg) **Repository** button from the left-hand sidebar then navigate to a folder)\n\n 2. Click on the ![Display Settings](./images/settings.svg) button at the top right of the item list\n\n 3. Click on the ![Remove Circle](./images/remove_circle_18dp.svg) button next to a field in the **Visible Columns** section\n\n 4. Click on the **Save** button\n\n
    \n\n\n### Image Thumbnail\n\nThe size of the preview image (thumbnail) is controlled by the **Row height** setting\n\n
    \n You can hover over the thumbnail with the cursor for a larger view\n
    \n\n
    \n\n To change the Row Height \n\n 1. Click on the ![Display Settings](./images/settings.svg) 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## 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\n
    \n\n To enable Compact List View \n\n 1. Navigate to any folder in the Repository (click on the ![Folder](./images/folder.svg) **Repository** button from the left-hand sidebar 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 (![List](./images/display-list.svg)), Compact List (![Compact List](./images/display-compact.svg)), or Icon (![Icon](./images/display-icon.svg))\n\n 3. In the popup menu, click **Compact List**\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\n
    \n\n To enable Icon View \n\n 1. Navigate to any folder in the Repository (click on the ![Folder](./images/folder.svg) **Repository** button from the left-hand sidebar 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 (![List](./images/display-list.svg)), Compact List (![Compact List](./images/display-compact.svg)), or Icon (![Icon](./images/display-icon.svg))\n\n 3. In the popup menu, click **Icon**\n\n
    \n\n
    \n\n To view metadata for an entry \n\n 1. Navigate to any folder in the Repository (click on the ![Folder](./images/folder.svg) **Repository** button from the left-hand sidebar 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 (or the bottom panel when viewing on a mobile device). You may need to click on the ![Collapsed](./images/sidebar-arrow-left.svg) button if the panel is collapsed\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\n
    \n\n To sort items in Icon View \n\n 1. Navigate to any folder in the Repository (click on the ![Folder](./images/folder.svg) **Repository** button from the left-hand sidebar then navigate to a folder)\n\n 2. Click on the ![Display Settings](./images/settings.svg) button at the top right of the item list\n\n 3. Select the desired sort option from the **Sort By** dropdown: **Name**, **Type**, or **Last Modified**\n\n
    \n","slug":"docs/repository/folder-listing"},{"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\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 ingestion 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 To upload file(s) using drag and drop \n\n 1. Navigate to any folder in the Repository (click on the ![Folder](./images/folder.svg) **Repository** button from the left-hand sidebar 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\n To upload file(s) using a file selection dialog \n\n 1. Navigate to any folder in the Repository (click on the ![Folder](./images/folder.svg) **Repository** button from the left-hand sidebar then navigate to a folder)\n\n 2. Click on the ![Actions](./images/block-add.svg) 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\n To 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\n To 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\n To 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 ![Folder](./images/folder.svg) 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\n To 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 To 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 Image formats that have multiple files per image (e.g. MRXS, VSI, AFI, NDPIS) must be packaged into a single archive file (e.g. tar) with the index files appearing at the root of the archive and all other related files and folders in the usual place relative to the index file. The system will automatically unpack these files after upload is complete.\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 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 Uploads section of the application, from where 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 Contact Pathcore Support to access the upload client and learn more.\n
    \n\n\n## Indexing Service\n##### \\[addon] \\[on-prem]\n\nThe indexing service has been designed for on-premise deployments. The service will find all the images in an attached storage system and reproduce the storage hierarchy in the Repository. The service provides a very efficient mechanism for managing storage in an on-premise deployment.\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 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":"Repository Operations","description":"repository operations"},"rawBody":"---\ntitle: Repository Operations\ndescription: repository operations\norder: 2\nsection: Repository\n---\n\n\n# Repository Operations\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 ![Down Arrow](./images/down-arrow-light.svg) button next to the item's name in the right-hand panel. You may need to click on the ![Collapsed](./images/sidebar-arrow-left.svg) button if the panel is collapsed.\n\n
    \n Depending on your Permissions and addons some operations may not be available.\n
    \n\n
    \n\n Move \n\n **Move** opens the Move Item dialog, allowing you to move the item (or items) to any accessible folder.\n\n 1. Right-click on the item (or items) to bring up the context menu\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
    \n\n Copy \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. Right-click on the item (or items) to bring up the context menu\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
    \n\n View 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\n Retry 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 recognised 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 Rename (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. Right-click on the item to bring up the context menu\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
    \n\n Edit Metadata \n\n **Edit Metadata** opens a dialog where you can add, change, or remove [Metadata](/docs/metadata/tags/) fields for the item (or items).\n\n 1. Right-click on the item (or items) to bring up the context menu\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/). See the [Metadata](/docs/metadata/tags/) section for more details\n\n
    \n\n
    \n\n Share (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
    \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. Right-click on the item to bring up the context menu\n\n 2. Click **Share**\n\n 3. The popup dialog allows you to add and manage share links. See [Managing Share Links](/docs/share-links/managing-share-links/) for more details\n\n
    \n\n
    \n\n Mark 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. Right-click on the item (or items) to bring up the context menu\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 Favorite / 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 See [Favorite Status](#favorite-status) for more details.\n\n 1. Right-click on the item (or items) to bring up the context menu\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\n Download \n\n **Download** opens the [Download](#downloading) dialog, allowing you to save items and metadata locally.\n\n 1. Right-click on the item (or items) to bring up the context menu\n\n 2. Click **Download**\n\n 3. In the popup dialog, select what you would like to download (files and/or metadata). See [Downloading](#downloading) for more details\n\n 4. Click on the **Download** button\n\n
    \n\n
    \n\n Open in VIS [addon] \n\n **Open in VIS** allows you to open the item (or items) in Visiopharm.\n\n 1. Right-click on the item (or items) to bring up the context menu\n\n 2. Click **Open in VIS**\n\n 3. In the popup dialog, select your options. See [Visiopharm Integration](/docs/integrations/visiopharm-integration/) for more details\n\n 4. Click on the **Open** button\n\n
    \n\n
    \n\n Open in HALO [addon] \n\n **Open in HALO** allows you to open the item (or items) in Indica Labs's HALO software.\n\n 1. Right-click on the item (or items) to bring up the context menu\n\n 2. Click **Open in HALO**\n\n 3. A SIS file will download\n\n 4. Open the SIS file in HALO. See [HALO Integration](/docs/integrations/halo-integration/) for more details\n\n
    \n\n
    \n\n Audit [addon] \n\n **Audit** opens the Audit Report dialog, which can generate a CSV file of changes made to the folder over a specified period of time.\n\n 1. Right-click on the item (or items) to bring up the context menu\n\n 2. Click **Audit**\n\n 3. In the popup dialog, select the start date from which you wish to see the audit data\n\n 4. Click on the **Download Audit** button to download a CSV file\n\n
    \n\n
    \n\n Delete \n\n **Delete** allows you to remove the folder and all of its contents from the Repository.\n\n
    \n Deleted items cannot be recovered. Be careful with this action.\n
    \n\n 1. Right-click on the item (or items) to bring up the context menu\n\n 2. Click **Delete**\n\n 3. Click on the **Yes** 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## 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\n
    \n\n To edit an item's description \n\n 1. Navigate to any folder in the Repository (click on the ![Folder](./images/folder.svg) **Repository** button from the left-hand sidebar 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 (or the bottom panel when viewing on a mobile device). You may need to click on the ![Collapsed](./images/sidebar-arrow-left.svg) 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\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\n
    \n The “read” status can be changed manually from the Context Menu for an item.\n
    \n\n\n## Favorite Status\n\nEach Repository item has a favorite status, which can be toggled by clicking on the ![Empty Star](./images/empty-star.svg) button adjacent to the item’s name. A solid star indicates an item has been marked as a favorite while a hollow star (default) status indicates the item is not a favorite.\n\nThe favorite status is unique for each user and can be toggled at any time, making it useful for tracking items that require further attention.\n\n
    \n\n To view a list of all favorited items \n\n 1. Click on the ![Star](./images/star.svg) **Starred** button in the **TAGS** section of the left-hand sidebar\n\n
    \n\n
    \n\n To toggle favorite status \n\n 1. Navigate to any folder in the Repository (click on the ![Folder](./images/folder.svg) **Repository** button from the left-hand sidebar then navigate to a folder)\n\n 2. Toggle the ![Empty Star](./images/empty-star.svg) button next to the item to indicate the status\n\n
    \n\n\n## Downloading\n\nIn general, one or more files or folders can be downloaded from the Repository. When downloading a single file, the download operation will be initiated in the normal way. When downloading multiple files and/or folders (or if you include any metadata), the download operation will be initiated in the normal way after the files/folders have been combined into an archive file.\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\n
    \n Some browsers may require your permission before downloading files.\n
    \n\n
    \n\n Download 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/) addon\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/) addon\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** / **.tar.gz** / **.zip**: This dropdown lets you select the archive format when more than one item and/or metadata are included\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\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\n
    \n\n To select more than one file \n\n 1. Navigate to any folder in the Repository (click on the ![Folder](./images/folder.svg) **Repository** button from the left-hand sidebar 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 To select more than one file in a continuous range \n\n 1. Navigate to any folder in the Repository (click on the ![Folder](./images/folder.svg) **Repository** button from the left-hand sidebar 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","slug":"docs/repository/repository-operations"},{"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\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 To export search results \n\n 1. Click on the ![Search](./images/search.svg) **Search** button from the left-hand sidebar\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 ![More](./images/more.svg) 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## 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":"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 fies, images and related information.\n\n\n## Built-in Image Viewer\n\nAny of the [supported image formats](/docs/repository/supported-formats/#supported-image-formats), such as whole slide images, DICOM images and photos, can be viewed with the built-in image 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","slug":"docs/repository/repository-overview"},{"frontmatter":{"title":"Supported Formats","description":"supported formats"},"rawBody":"---\ntitle: Supported Formats\ndescription: supported formats\norder: 4\nsection: Repository\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
    \n\n List of supported formats \n\n | Vendor | Format | Status |\n | ----------- | ---------- | ------------ |\n | 3D Histech | MRXS | Full Support |\n | Aperio | SVS | Full Support |\n | Aperio | AFI | Full Support |\n | Hamamatsu | VMS | Full Support |\n | Hamamatsu | VMU | Full Support |\n | Hamamatsu | NDPI | Full Support |\n | Hamamatsu | NDPIS | Full Support |\n | Leica | SCN | Full Support |\n | Motic | Motic SVS | Full Support |\n | Olympus | VSI | Full Support |\n | OME | OME TIFF | Full Support |\n | PerkinElmer | QPTIFF | Full Support |\n | Sakura | SVSlide | Full Support |\n | Ventana | BIF | Full Support |\n | Ventana | TIF | Full Support |\n | Zeiss | CZI | Full Support |\n | | Tiled TIFF | Full Support |\n | | BigTIFF | Full Support |\n | | JPEG2000 | Full Support |\n | | DICOM | Full Support |\n | | BMP | Full Support |\n | | JFIF | Full Support |\n | | PNG | Full Support |\n\n
    \n","slug":"docs/repository/supported-formats"},{"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\n
    \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\n
    \n\n To save a search query \n\n 1. Click on the ![Search](./images/search.svg) **Search** button from the left-hand sidebar\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 To execute a previously saved search query \n\n 1. Click on the ![Search](./images/search.svg) **Search** button from the left-hand sidebar\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## 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\n
    \n\n To share a saved search with your team \n\n 1. Click on the ![Search](./images/search.svg) **Search** button from the left-hand sidebar\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## 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\n
    \n\n To rename a saved search query \n\n 1. Click on the ![Search](./images/search.svg) **Search** button from the left-hand sidebar\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\n To delete a saved search query \n\n 1. Click on the ![Search](./images/search.svg) **Search** button from the left-hand sidebar\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","slug":"docs/search/saved-searches"},{"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 NULL 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 access the Data Groups tab in Settings\n- Cannot access the Data Group dropdown during user creation\n- Will not see the Accessible Content column in the users table\n- Cannot Edit Accessible Content menu option in the users table\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##### [BioPharma]\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 [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 To set the result type preamble \n\n 1. Click on the ![Search](./images/search.svg) **Search** button from the left-hand sidebar\n\n 2. Choose one or more types from the **Find** dropdown\n\n
    \n\n
    \n\n To set the location preamble \n\n 1. Click on the ![Search](./images/search.svg) **Search** button from the left-hand sidebar\n\n 2. Click on the ![Edit](./images/edit.svg) 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## 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\n
    \n\n To create a basic search query \n\n 1. Click on the ![Search](./images/search.svg) **Search** button from the left-hand sidebar\n\n 2. (Optional) Configure the [result type preamble](#search-preambles) from the **Find** dropdown\n\n 3. (Optional) Configure the [location preamble](#search-preambles) from the ![Edit](./images/edit.svg) dropdown\n\n 4. (Optional) Configure the logical operator from the **Matching** dropdown\n\n 5. Click on the **+ Condition** button; repeat as necessary\n\n a. Select a field from the dropdown\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## Advanced Queries\n\nAdvanced search can be fully customized and may include logical groups (i.e. bracketed expressions).\n\n
    \n\n To create an advanced search query \n\n 1. Click on the ![Search](./images/search.svg) **Search** button from the left-hand sidebar\n\n 2. (Optional) Configure the [result type preamble](#search-preambles) from the **Find** dropdown\n\n 3. (Optional) Configure the [location preamble](#search-preambles) from the ![Edit](./images/edit.svg) dropdown\n\n 4. (Optional) Configure the logical operator from the **Matching** dropdown\n\n 5. Click on the **+ Condition** button; repeat as necessary\n\n a. Select a field from the dropdown\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","slug":"docs/search/search-overview"},{"frontmatter":{"title":"Search Operations","description":"saved operations"},"rawBody":"---\ntitle: Search Operations\ndescription: saved operations\norder: 11\nsection: Search\n---\n\n\n# Search Operations\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 ![Down Arrow](./images/down-arrow-light.svg) button next to the item's name in the right-hand panel. You may need to click on the ![Collapsed](./images/sidebar-arrow-left.svg) button if the panel is collapsed.\n\n
    \n Depending on your Permissions and addons some operations may not be available.\n
    \n\n
    \n\n Move \n\n **Move** opens the Move Item dialog, allowing you to move the item (or items) to any accessible folder.\n\n 1. Right-click on the item (or items) to bring up the context menu\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
    \n\n Copy \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. Right-click on the item (or items) to bring up the context menu\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
    \n\n View 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\n Retry 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 recognised 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 Rename (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. Right-click on the item to bring up the context menu\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
    \n\n Edit Metadata \n\n **Edit Metadata** opens a dialog where you can add, change, or remove [Metadata](/docs/metadata/tags/) fields for the item (or items).\n\n 1. Right-click on the item (or items) to bring up the context menu\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/). See the [Metadata](/docs/metadata/tags/) section for more details\n\n
    \n\n
    \n\n Share (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
    \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. Right-click on the item to bring up the context menu\n\n 2. Click **Share**\n\n 3. The popup dialog allows you to add and manage share links. See [Managing Share Links](/docs/share-links/managing-share-links/) for more details\n\n
    \n\n
    \n\n Mark 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. Right-click on the item (or items) to bring up the context menu\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 Favorite / 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 See [Favorite Status](/docs/repository/repository-operations/#favorite-status) for more details.\n\n 1. Right-click on the item (or items) to bring up the context menu\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\n Download \n\n **Download** opens the [Download](/docs/repository/repository-operations/#downloading) dialog, allowing you to save items and metadata locally.\n\n 1. Right-click on the item (or items) to bring up the context menu\n\n 2. Click **Download**\n\n 3. In the popup dialog, select what you would like to download (files and/or metadata). See [Downloading](/docs/repository/repository-operations/#downloading) for more details\n\n 4. Click on the **Download** button\n\n
    \n\n
    \n\n Open in VIS [addon] \n\n **Open in VIS** allows you to open the item (or items) in Visiopharm.\n\n 1. Right-click on the item (or items) to bring up the context menu\n\n 2. Click **Open in VIS**\n\n 3. In the popup dialog, select your options. See [Visiopharm Integration](/docs/integrations/visiopharm-integration/) for more details\n\n 4. Click on the **Open** button\n\n
    \n\n
    \n\n Open in HALO [addon] \n\n **Open in HALO** allows you to open the item (or items) in Indica Labs's HALO software.\n\n 1. Right-click on the item (or items) to bring up the context menu\n\n 2. Click **Open in HALO**\n\n 3. A SIS file will download\n\n 4. Open the SIS file in HALO. See [HALO Integration](/docs/integrations/halo-integration/) for more details\n\n
    \n\n
    \n\n Audit [addon] \n\n **Audit** opens the Audit Report dialog, which can generate a CSV file of changes made to the folder over a specified period of time.\n\n 1. Right-click on the item (or items) to bring up the context menu\n\n 2. Click **Audit**\n\n 3. In the popup dialog, select the start date from which you wish to see the audit data\n\n 4. Click on the **Download Audit** button to download a CSV file\n\n
    \n\n
    \n\n Delete \n\n **Delete** allows you to remove the folder and all of its contents from the Repository.\n\n
    \n Deleted items cannot be recovered. Be careful with this action.\n
    \n\n 1. Right-click on the item (or items) to bring up the context menu\n\n 2. Click **Delete**\n\n 3. Click on the **Yes** 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## 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\n
    \n\n To apply tags to all search results \n\n 1. Click on the ![Search](./images/search.svg) **Search** button from the left-hand sidebar\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 ![More](./images/more.svg) 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. 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","slug":"docs/search/search-operations"},{"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\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 To create a data group \n\n 1. Click on the ![Settings](./images/settings.svg) **Settings** button from the left-hand sidebar\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## Modifying Data Groups\n\nModifying a data group immediately affects all users that are associated with it.\n\n
    \n\n To modify a data group \n\n 1. Click on the ![Settings](./images/settings.svg) **Settings** button from the left-hand sidebar\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## 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\n
    \n\n To delete a data group \n\n 1. Click on the ![Settings](./images/settings.svg) **Settings** button from the left-hand sidebar\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","slug":"docs/settings/data-groups"},{"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\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 picture and signature. Users cannot change their email address.\n\n
    \n\n To 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\n To add or change the profile picture 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 to in the Profile Picture section\n\n 5. Click on the **Add Profile Photo** button and select an image from your PC\n\n 6. (Optional) Use the slide beneath the picture to adjust the visible content\n\n 7. Click on the **Apply** button to save your changes\n\n
    \n\n
    \n\n To 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 To 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\n\n
    \n\n\n## Preferences\n\n### Visiopharm Preferences [addon]\n\n
    \n\n To 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 To 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\n
    \n","slug":"docs/settings/my-account"},{"frontmatter":{"title":"Permissions","description":"permissions"},"rawBody":"---\ntitle: Permissions\ndescription: permissions\norder: 40\nsection: Settings\n---\n\n\n# Permissions\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\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\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 Health Information (PHI) 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 Health Information (PHI) flag and slide labels. |\n","slug":"docs/settings/permissions"},{"frontmatter":{"title":"Roles","description":"roles"},"rawBody":"---\ntitle: Roles\ndescription: roles\norder: 41\nsection: Settings\n---\n\n\n# Roles\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 pre-defined 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 permission except for team-level permissions\n- **Viewer**: has permissions to view and download files and metadata but cannot edit or delete any data\n- **Anonymized Viewer**: has all the permission of the Viewer except for the View PHI permission\n\n
    \n\n To view system roles \n\n 1. Click on the ![Settings](./images/settings.svg) **Settings** button from the left-hand sidebar\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## Custom Roles [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\n
    \n\n To create a new custom role \n\n 1. Click on the ![Settings](./images/settings.svg) **Settings** button from the left-hand sidebar\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 to finish\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\n
    \n System roles cannot be modified.\n
    \n\n
    \n\n
    \n\n To edit a non-system role \n\n 1. Click on the ![Settings](./images/settings.svg) **Settings** button from the left-hand sidebar\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 to finish\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\n
    \n System roles cannot be deleted.\n
    \n\n
    \n\n
    \n\n To delete a non-system role \n\n 1. Click on the ![Settings](./images/settings.svg) **Settings** button from the left-hand sidebar\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","slug":"docs/settings/roles"},{"frontmatter":{"title":"Storage Statistics","description":"storage statistics"},"rawBody":"---\ntitle: Storage Statistics\ndescription: storage statistics\norder: 45\nsection: Settings\n---\n\n\n# Storage Statistics\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 To view storage statistics \n\n 1. Click on the ![Settings](./images/settings.svg) **Settings** button from the left-hand sidebar\n\n 2. Click on the **Storage** tab\n\n
    \n","slug":"docs/settings/storage-statistics"},{"frontmatter":{"title":"Team Customization","description":"team customization"},"rawBody":"---\ntitle: Team Customization\ndescription: team customization\norder: 44\nsection: Settings\n---\n\n\n# Team Customization\n\n
    \n\nEach team has a customizable name and logo that appear in the top left corner of the screen while on the repository page.\n\n
    \n The Manage team permission flag is required to change the team name and logo.\n
    \n\n\n## Team Name\n\n
    \n\n To change team name \n\n 1. Click on the ![Settings](./images/settings.svg) **Settings** button from the left-hand sidebar\n\n 2. Click on the **Team Customization** tab\n\n 3. Click on **Edit** next to Team Name\n\n 4. Type a new name in the Team Name field\n\n 5. Click on **Save** to finish\n\n
    \n\n\n## Team Logo\n\n
    \n Maximum file size for a logo is 10 MiB.\n
    \n\n
    \n\n
    \n\n To add/change team logo \n\n 1. Click on the ![Settings](./images/settings.svg) **Settings** button from the left-hand sidebar\n\n 2. Click on the **Team Customization** tab\n\n 3. Click on **Add** or **Edit** next to Team Logo\n\n 4. Click on the **Choose File** button\n\n 5. Select a file from the computer\n\n 6. Click on the **Update Logo** button to finish\n\n
    \n\n
    \n\n To remove the team logo \n\n 1. Click on the ![Settings](./images/settings.svg) **Settings** button from the left-hand sidebar\n\n 2. Click on the **Team Customization** tab\n\n 3. Click on **Edit** next to Team Logo\n\n 4. Click on the **Remove Logo** button to remove\n\n
    \n","slug":"docs/settings/team-customization"},{"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\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, pending 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 To view the list of accounts currently registered, and their properties \n\n 1. Click on the ![Settings](./images/settings.svg) **Settings** button from the left-hand sidebar\n\n 2. Click on the **Users** tab\n\n
    \n\n
    \n\n To search for an existing user account by name or email address \n\n 1. Click on the ![Settings](./images/settings.svg) **Settings** button from the left-hand sidebar\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 To show/hide accounts that are not active \n\n 1. Click on the ![Settings](./images/settings.svg) **Settings** button from the left-hand sidebar\n\n 2. Click on the **Users** tab\n\n 3. Click on the ![Filter](./images/filter.svg) **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\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 “pending activation” and the new user will not be able to log in until [Account Activation](#account-activation) is completed.\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 To create a user account \n\n 1. Click on the ![Settings](./images/settings.svg) **Settings** button from the left-hand sidebar\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; 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; 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\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\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 To resend a user account activation notification \n\n 1. Click on the ![Settings](./images/settings.svg) **Settings** button from the left-hand sidebar\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\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\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 To modify the permission/role associated with a user’s account \n\n 1. Click on the ![Settings](./images/settings.svg) **Settings** button from the left-hand sidebar\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; 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### 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\n
    \n\n To modify the accessible content or the data group associated with user accounts \n\n 1. Click on the ![Settings](./images/settings.svg) **Settings** button from the left-hand sidebar\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; 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### 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\n
    \n\n To invalidate a user’s session \n\n 1. Click on the ![Settings](./images/settings.svg) **Settings** button from the left-hand sidebar\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### 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 audit records 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\n
    \n\n To disable a user account or to enable a previously disabled account \n\n 1. Click on the ![Settings](./images/settings.svg) **Settings** button from the left-hand sidebar\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","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\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 tag and behaves like embedded maps that are commonly used on many websites.\n\nEmbedded images are powered by share links and have the same restrictions and behave in a similar fashion. The embed code retrieved from the Viewer provides additional flexibility — primarily the ability to control the recipient's initial view. However, the initial view for embedded images may be affected by the size of the window that renders the image.\n\n
    \n Embedded images may not work in browsers that restrict third-party cookies.\n
    \n\n
    \n\n To retrieve the embed code for an image from the Repository \n\n 1. Navigate to any folder in the Repository (click on the ![Folder](./images/folder.svg) **Repository** button from the left-hand sidebar then navigate to a folder)\n\n 2. Right-click on the image to bring up the context menu\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 ![Copy to Clipboard](./images/clipboard.svg) 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\n To 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 ![Share](./images/viewer-share.svg) 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 ![Copy to Clipboard](./images/clipboard.svg) 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","slug":"docs/share-links/embedding-an-image"},{"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##### [addon]\n\n
    \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\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 To download logs of regions viewed for a share link \n\n 1. Navigate to any folder in the Repository (click on the ![Folder](./images/folder.svg) **Repository** button from the left-hand sidebar then navigate to a folder)\n\n 2. Right-click on the item to bring up the context menu\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](./images/download.svg) **Download Data** button underneath the **Track view history** toggle\n\n
    \n\n
    \n\n To 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 ![Folder](./images/folder.svg) **Repository** button from the left-hand sidebar then navigate to a folder)\n\n 2. Right-click on the item to bring up the context menu\n\n 3. Click **Share**\n\n 4. In the popup dialog, click on the ![Download](./images/download.svg) button to the right of the **New Share Link** button\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 DataType 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\n
    \n\n Example 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://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://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\n Example 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","slug":"docs/share-links/advanced-share-link-options"},{"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, right-click on the item in the Repository and select **Share** from the context menu. 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 To edit a share link for the current folder from the Repository \n\n 1. Navigate to any folder in the Repository (click on the ![Folder](./images/folder.svg) **Repository** button from the left-hand sidebar then navigate to a folder)\n\n 2. Click on the ![Share](./images/share.svg) 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 ![Copy to Clipboard](./images/clipboard.svg) 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\n To delete a share link for the current folder from the Repository \n\n 1. Navigate to any folder in the Repository (click on the ![Folder](./images/folder.svg) **Repository** button from the left-hand sidebar then navigate to a folder)\n\n 2. Click on the ![Share](./images/share.svg) 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 ![Delete](./images/delete.svg) 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\n To edit a share link for any item from the Repository \n\n 1. Navigate to any folder in the Repository (click on the ![Folder](./images/folder.svg) **Repository** button from the left-hand sidebar then navigate to a folder)\n\n 2. Right-click on the item to bring up the context menu\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 ![Copy to Clipboard](./images/clipboard.svg) 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\n To delete a share link for any item from the Repository \n\n 1. Navigate to any folder in the Repository (click on the ![Folder](./images/folder.svg) **Repository** button from the left-hand sidebar then navigate to a folder)\n\n 2. Right-click on the item to bring up the context menu\n\n 3. Click **Share**\n\n 4. In the popup dialog, click on the ![Delete](./images/delete.svg) 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\n To 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 ![Share](./images/viewer-share.svg) 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 ![Copy to Clipboard](./images/clipboard.svg) 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\n To 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 ![Share](./images/viewer-share.svg) button in the left sidebar\n\n 3. In the popup dialog, click on the ![Delete](./images/delete.svg) 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","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\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 To 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\n To 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## 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. For any image where magnification can not be determined, the magnification controls are replaced with scaling controls (e.g. 50%, 100%).\n\n
    \n The current magnification is displayed in the Viewer top bar\n
    \n\n
    \n\n To 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 To 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### 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## Focal Planes\n\nFocal planes are automatically detected when present in supported images. If the image has multiple [sub-images](/docs/viewer/image-settings/#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\n
    \n\n To 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 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 ![Up Arrow](./images/up-arrow.svg) and ![Down Arrow](./images/down-arrow.svg) 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 To change the focal plane using the mouse \n\n 1. Click on the ![Up Arrow](./images/up-arrow.svg) or ![Down Arrow](./images/down-arrow.svg) buttons on the focal plane controls\\*\n\n\n \\* The focal plane controls consist of ![Up Arrow](./images/up-arrow.svg) and ![Down Arrow](./images/down-arrow.svg) 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 To 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## 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\n\n
    \n\n To 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 ![Expand Toolbar](./images/expand.svg) button to expand the toolbar if necessary\n\n 3. Click on the ![Rotate](./images/rotate.svg) button in the toolbar to show or hide the rotation tool\n\n
    \n\n
    \n\n To 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
    \n\n To 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\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\n
    \n Color Management is available for RGB images and disabled by default; users can choose their preference.\n
    \n\n
    \n\n To 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 ![Expand Toolbar](./images/expand.svg) button to expand the toolbar if necessary\n\n 3. Click on the ![Palette](./images/palette.svg) button dropdown 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## Full Screen Mode\n\nTo enlarge the image viewport, so that it fills your screen, click on the ![Fullscreen](./images/fullscreen.svg) 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":"Annotations Panel","description":"annotations panel"},"rawBody":"---\ntitle: Annotations Panel\ndescription: annotations panel\nsection: Viewer\norder: 19\n---\n\n\n# Annotations Panel\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 To 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 ![Annotations](./images/edit.svg) button in the left sidebar to open the Annotations panel\n\n
    \n\n\n## Creating Annotations\n\n
    \n\n 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\n
    \n\nThe following annotation types are available:\n\n| Tool | Instruction to create |\n| -------- | ------------------------------------------------------------ |\n| Rect | Hold and drag to contain an area of interest. |\n| Arrow | Hold and drag to point to an area of interest. The starting point will be the arrowhead. |\n| Polygon | Click to add points.
    Click 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 | Hold and drag to draw on the image. |\n| Ruler | Hold and drag to measure the area of interest. |\n| Ellipse | Hold and drag to contain the area of interest. The starting point will be the center of the ellipse. |\n| Bookmark | Click/tap to place an area of interest to place a bookmark pin on the image. |\n\n\n### Deleting Annotations\n\nAnnotations can be deleted from within the Viewer or from the Annotations panel.\n\n
    \n\n To 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 ![Delete](./images/delete.svg) button at the bottom right of the popup dialog\n\n 3. Click on the **OK** button to confirm\n\n
    \n\n
    \n\n To 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 ![Annotations](./images/edit.svg) button in the left sidebar\n\n 3. Identify the annotation entry to be deleted in the list\n\n 4. Click on the ![Delete](./images/delete.svg) button\n\n 5. Click on the **OK** button to confirm\n\n
    \n\n\n## Editing Annotations\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\n
    \n\n To 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 To 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 ![Annotations](./images/edit.svg) 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### 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\n
    \n\n To 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 To 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 ![Annotations](./images/edit.svg) 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### 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\n
    \n\n To 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 To 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 ![Annotations](./images/edit.svg) 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### 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\n
    \n\n To 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 ![Annotations](./images/edit.svg) button in the left sidebar\n\n 3. Identify the annotation entry to be modified\n\n 4. Click on the ![Eye](./images/eye.svg) button to toggle visibility\n\n
    \n\n
    \n\n To 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 ![Annotations](./images/edit.svg) button in the left sidebar\n\n 3. Click on the ![Eye](./images/eye.svg) button at the top right corner of the Annotations panel to toggle visibility for all annotations\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 ![Lock](./images/lock.svg) button at the top right corner of the Annotations panel.\n\n
    \n\n To 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 ![Annotations](./images/edit.svg) button in the left sidebar\n\n 3. Identify the annotation entry to be modified\n\n 4. Click on the ![private](./images/private.svg) button to toggle the annotation’s sharing mode\n\n
    \n\n\n### Locating an Annotation\n\nWhile on the Viewer, annotations are easily visible and accessible.\n\n
    \n\n To 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 ![Annotations](./images/edit.svg) button in the left sidebar\n\n 3. Identify the annotation entry\n\n 4. Click on the ![Jump to Annotation](./images/gps.svg) button to jump to the annotation in the Viewer\n\n
    \n","slug":"docs/viewer/annotations-panel"},{"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\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 To create an image share link from the Repository \n\n 1. Navigate to any folder in the Repository (click on the ![Folder](./images/folder.svg) **Repository** button from the left-hand sidebar then navigate to a folder)\n\n 2. Right-click on the image to bring up the context menu\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 ![Copy to Clipboard](./images/clipboard.svg) 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 To 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 ![Share](./images/viewer-share.svg) 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 ![Copy to Clipboard](./images/clipboard.svg) 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## 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\n
    \n\n To create a share link for the current folder \n\n 1. Navigate to any folder in the Repository (click on the ![Folder](./images/folder.svg) **Repository** button from the left-hand sidebar then navigate to a folder)\n\n 2. Click on the ![Down Arrow](./images/down-arrow-light.svg) 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 ![Copy to Clipboard](./images/clipboard.svg) 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 To create a share link for a folder \n\n 1. Navigate to any folder in the Repository (click on the ![Folder](./images/folder.svg) **Repository** button from the left-hand sidebar then navigate to a folder)\n\n 2. Right-click on the folder to bring up the context menu\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 ![Copy to Clipboard](./images/clipboard.svg) 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## 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\n
    \n\n To create a share link for an attachment \n\n 1. Navigate to any folder in the Repository (click on the ![Folder](./images/folder.svg) **Repository** button from the left-hand sidebar then navigate to a folder)\n\n 2. Right-click on the item to bring up the context menu\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 ![Copy to Clipboard](./images/clipboard.svg) 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## 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 PHI 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\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":"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\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 ![Folder](./images/folder.svg) button located on the left-hand sidebar of the Viewer.\n\n
    \n\n To 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 ![Folder](./images/folder.svg) button in the left sidebar to open the Browse Folder panel\n\n
    \n\n
    \n\n To 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 ![Folder](./images/folder.svg) 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 To 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 ![Folder](./images/folder.svg) button in the left sidebar\n\n 3. Click on the ![Open in New Tab](./images/open-new.svg) button to the right of the folder name\n\n
    \n\n\n## List Mode\n\nThe Browse Folder panel can list items using three formats: List, Compact List, and Icon.\n\n
    \n\n To 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 ![Folder](./images/folder.svg) 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 (![List](./images/display-list.svg)), Compact List (![Compact List](./images/display-compact.svg)), or Icon (![Icon](./images/display-icon.svg))\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## Sort Order\n\nThe list of items in the Browse Folder panel can be sorted by any metadata field.\n\n
    \n\n To 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 ![Folder](./images/folder.svg) 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 ![Up Arrow](./images/sort-up-arrow.svg) ascending order or ![Down Arrow](./images/sort-down-arrow.svg) descending order\n\n
    \n\n\n## Name Filter\n\nThe list of items can be filtered by name for quicker browsing.\n\n
    \n\n To filter the list \n\n 1. Click in the search box indicated by the ![Magnifying Glass](./images/viewer-search.svg) 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\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\n
    \n\n To toggle the read status \n\n 1. Right-click on any entry in the Browse Folder panel to bring up the context menu\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 To 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## 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\n
    \n\n To toggle the favorite status \n\n 1. Click on the ![Empty Star](./images/viewer-empty-star.svg) 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 ![Star](./images/viewer-star.svg) button to the left of an item name in the Browse Folder panel to remove the tag\n\n
    \n\n
    \n\n To 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","slug":"docs/viewer/browse-folder-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\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 To maximize the overview tool \n\n 1. Click on the ![Open](./images/open.svg) **Overview** button on the bottom right corner of the image\n\n
    \n\n\n
    \n\n To minimize the overview tool \n\n 1. Click on the ![Hide](./images/hide.svg) button on the top left corner of the overlay tool\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\n
    \n\n To toggle the visibility of the heatmap \n\n 1. Click on the ![Overview](./images/overview.svg) button to the top left of the overview tool\n\n
    \n\n
    \n\n To 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 ![Help](./images/help.svg) 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","slug":"docs/viewer/overview-tool"},{"frontmatter":{"title":"Image Settings","description":"image settings"},"rawBody":"---\ntitle: Image Settings\ndescription: image settings\norder: 21\nsection: Viewer\n---\n\n\n# Image Settings\n\n
    \n\nThe Image Settings panel can be used to alter the rendering of multi-channel images in the Viewer.\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\n
    \n\n To adjust the visibility of sub-images \n\n 1. From within the Viewer, click on the ![Layers](./images/layers.svg) button at the bottom left of the Viewer to reveal the Image Settings dialog\n\n 2. Click on the ![Eye](./images/eye.svg) 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 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## 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\n
    \n\n To adjust the visibility of an image channel \n\n 1. From within the Viewer, click on the ![Layers](./images/layers.svg) button at the bottom left of the Viewer to reveal the Image Settings dialog\n\n 2. Click on the ![Eye](./images/eye.svg) 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 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## 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\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### Pseudocolor\n\nThe default color of each channel can be modified to any RGB value.\n\n
    \n\n To change the pseudocolor of a channel \n\n 1. From within the Viewer, click on the ![Layers](./images/layers.svg) 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 To reset the pseudocolor of a channel to its default value \n\n 1. From within the Viewer, click on the ![Layers](./images/layers.svg) button at the bottom left of the Viewer to reveal the Image Settings dialog\n\n 2. Click on the ![Undo](./images/undo.svg) 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### 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\n\n
    \n\n To adjust the histogram \n\n 1. From within the Viewer, click on the ![Layers](./images/layers.svg) 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 To reset the histogram to its default value \n\n 1. From within the Viewer, click on the ![Layers](./images/layers.svg) 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 ![Undo](./images/undo.svg) 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","slug":"docs/viewer/image-settings"},{"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##### [addon]\n\n
    \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\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\n To create a Figure from 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 ![Menu](./images/menu.svg) 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 Figure** dialog that pops up, navigate to a folder using the folder browser (by default the selected folder is the folder used last)\n\n 6. Enter a **File name** in the text box at the bottom left\n\n 7. Click on the **Save to Folder** 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\n To 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 ![Menu](./images/menu.svg) 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\n To open a previously saved Figure \n\n 1. Navigate to any folder in the Repository (click on the ![Folder](./images/repository-folder.svg) **Repository** button from the left-hand sidebar then navigate to a folder)\n\n 2. Click on an item with the ![Figure](./images/repository-figure.svg) 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\n To rename a Figure from the Viewer \n\n 1. Click on the ![Edit](./images/edit.svg) icon next to the current name of the Figure at the top left of the Viewer (defaults to \"Untitled View\")\n\n 2. Type the new name for the Figure\n\n
    \n\n
    \n\n To rename a Figure from the Repository \n\n 1. Navigate to any folder in the Repository (click on the ![Folder](./images/repository-folder.svg) **Repository** button from the left-hand sidebar then navigate to a folder)\n\n 2. Right click on an item with the ![Figure](./images/repository-figure.svg) 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\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\n
    \n Annotations can only be created when annotations on the panel are visible.\n
    \n\n
    \n\n To 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 ![Expand Toolbar](./images/expand.svg) button to expand the toolbar if necessary\n\n 3. Click on the ![Pen](./images/edit.svg) 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
    \n\n To 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### Slide Label\n\nThe slide label can be overlaid on an image panel and made visible until it's removed.\n\n
    \n\n To 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 ![Expand Toolbar](./images/expand.svg) button to expand the toolbar if necessary\n\n 3. Click on the ![Pen](./images/edit.svg) 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 ![Rotate](./images/rotate.svg) 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### Text Label\n\nA text label can be overlaid on an image panel and made visible until it’s removed.\n\n
    \n\n To 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 ![Expand Toolbar](./images/expand.svg) button to expand the toolbar if necessary\n\n 3. Click on the ![Pen](./images/edit.svg) 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 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### Scale Bar\n\nA scale bar can be overlaid on an image panel and made visible until it’s removed.\n\n
    \n\n To 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 ![Expand Toolbar](./images/expand.svg) button to expand the toolbar if necessary\n\n 3. Click on the ![Pen](./images/edit.svg) 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\n 6. (Optional) Select the location of the measurement text relative to the scale bar by clicking one of the **Text Alignment** options: ![Align Left](./images/align-left.svg) (left), ![Align Center](./images/align-center.svg) (center), or ![Align Right](./images/align-right.svg) (right)\n 7. (Optional) Click on **Apply to All Slides** to apply these settings to all panels\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\n
    \n\n To export a Figure from the Repository \n\n 1. Navigate to any folder in the Repository (click on the ![Folder](./images/repository-folder.svg) **Repository** button from the left-hand sidebar then navigate to a folder)\n\n 2. Select a Figure object from the folder listing\n\n 3. Right-click on the item to bring up the context menu\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\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## Deleting Figures\n\nFigures can be deleted from the Repository or from within the Viewer.\n\n
    \n\n To delete a Figure from the Repository \n\n 1. Navigate to any folder in the Repository (click on the ![Folder](./images/repository-folder.svg) **Repository** button from the left-hand sidebar then navigate to a folder)\n\n 2. Select a Figure object from the folder listing\n\n 3. Right-click on the item to bring up the context menu\n\n 4. Click on **Delete**\n\n 5. Click on the **Yes** button to confirm\n\n
    \n\n
    \n\n To delete a Figure from within the Viewer \n\n 1. Open the Figure in the Viewer\n\n 2. Click on the ![Menu](./images/menu.svg) icon at the right corner of the Viewer top bar\n\n 3. Select **Delete Figure** from the dropdown menu\n\n 5. Click on the **Yes** button to confirm\n\n
    \n","slug":"docs/viewer/figure-maker"},{"frontmatter":{"title":"Snapshots","description":"snapshots"},"rawBody":"---\ntitle: Snapshots\ndescription: snapshots\norder: 20\nsection: Viewer\n---\n\n\n# Snapshots\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 [Information Panel](/docs/viewer/information-panel/) and from the Metadata tab in the [Folder Listing](/docs/repository/folder-listing/).\n\n
    \n\n To 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 ![Snapshot](./images/snapshot.svg) 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 To 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 ![Info](./images/info.svg) 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## 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\n
    \n\n To 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\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 To download a snapshot from the 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 ![Info](./images/info.svg) 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\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## 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\n
    \n\n To 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\n To 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 To 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\n\n 7. (Optional) Select the location of the measurement text relative to the scale bar from the **Text Alignment** dropdown (auto, left, center, or right)\n\n
    \n\n\n## Snapshot Properties\n\n### Snapshot Name\n\nThe name is a single line text field that supports unicode characters. The name can be changed from within the Viewer or from the Information panel.\n\n
    \n\n To 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 To rename a snapshot from the 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 ![Info](./images/info.svg) 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### 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\n
    \n\n To 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### 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\n
    \n\n To 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 ![Info](./images/info.svg) button in the left sidebar\n\n 3. Scroll down to the **Snapshots** section\n\n 4. Click on the ![Eye](./images/eye.svg) button, adjacent to the **Snapshots** title, to toggle visibility for all snapshots\n\n
    \n\n\n## Deleting Snapshots\n\nSnapshots can be deleted from within the Viewer or from the Information panel.\n\n
    \n\n To 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\n To delete a snapshot from the 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 ![Info](./images/info.svg) 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","slug":"docs/viewer/snapshots"},{"frontmatter":{"title":"Information Panel","description":"information panel"},"rawBody":"---\ntitle: Information Panel\ndescription: information panel\norder: 17\nsection: Viewer\n---\n\n\n# Information Panel\n\n
    \n\nThe file 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 To 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 ![Info](./images/info.svg) button in the left sidebar to open the Information panel\n\n
    \n\n\n## Image (Slide) Label\n\nIf a slide label is available, it will be displayed at the top of the information panel.\n\n
    \n Slide label may contain PHI and as such, the label is hidden for users that do not have the “View Protected Health Information” permission flag.\n
    \n\n
    \n\n To 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 ![Info](./images/info.svg) button in the left sidebar\n\n
    \n\n
    \n\n To rotate the slide label \n\n 1. Hover over the label with the mouse\n\n 2. Click on the ![Rotate](./images/rotate.svg) button until the desired orientation is achieved\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 information panel.\n\n
    \n\n To 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 ![Info](./images/info.svg) 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 field\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 To 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 ![Info](./images/info.svg) button in the left sidebar\n\n 3. Click on the **X** button of the relevant tag\n\n
    \n\n\n## Image Description\n\nA description can be added to an image which will be visible to all users.\n\n
    \n\n To 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 ![Info](./images/info.svg) 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\n## Image Metadata and Fields\n\nAll of the metadata fields associated with the file are listed in the information panel. You can click on a custom field metadata value to jump to a search using that criteria.\n\n
    \n Metadata fields that are marked with “May contain PHI” will be hidden (field value will be “Anonymized”) for users that do not have “View Protected Health Information” permission.\n
    \n\n
    \n\n To edit file 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 ![Info](./images/info.svg) 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 and select a field from the dropdown\n\n 6. (Optional) Change the value(s) of the listed field(s) accordingly, or clear the value by clicking on the grey **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\n## Downloading an Image\n\nOnly users with the “Download File” and “Download Image” permission flag are able to download files and images, respectively.\n\n
    \n\n To 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 ![Info](./images/info.svg) 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\n## Deleting an Image\n\nOnly users with the “Delete File” permission flag are able to delete images.\n\n
    \n\n To delete the currently open and selected 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 ![Info](./images/info.svg) button in the left sidebar\n\n 3. Click on the image name\n\n 4. Click on **Delete** in the dropdown menu\n\n 5. Click on the **OK** button to confirm\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 Information panel.\n\n
    \n\n To 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 ![Info](./images/info.svg) 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\n To 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 ![Info](./images/info.svg) 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\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 To 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 ![Info](./images/info.svg) 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
    \n\n To 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 ![Info](./images/info.svg) 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","slug":"docs/viewer/information-panel"},{"frontmatter":{"title":"Overview","description":"overview"},"rawBody":"---\ntitle: Overview\ndescription: overview\norder: 14\nsection: Viewer\n---\n\n\n# Overview\n\n
    \n\nWhen you click on an image in a folder, Flow will open the Viewer. The Viewer is optimized for viewing whole slide images and supports a range of [image formats](/docs/repository/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","slug":"docs/viewer/overview"},{"frontmatter":{"title":"Overlays","description":"overlays"},"rawBody":"---\ntitle: Overlays\ndescription: overlays\norder: 22\nsection: Viewer\n---\n\n\n# Overlays\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 last entry in the panel is visually on top 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\n Attach 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 ![Overlays](./images/layers.svg) button in the left sidebar\n\n 3. Upload an image from your computer by dragging a [supported image](/docs/repository/supported-formats/#supported-image-formats) file onto the sidebar\n\n
    \n\n
    \n\n Attach 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 ![Overlays](./images/layers.svg) 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. (Optional) Once the upload is complete, click on the **Edit Metadata** button to edit the metadata or the **Edit** button to change the name\n\n 6. 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### Deleting Overlays\n\nOverlays can be deleted from the Overlays panel.\n\n
    \n\n To 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 ![Overlays](./images/layers.svg) button in the left sidebar\n\n 3. Identify the overlay entry to be modified\n\n 4. Click on the ![Delete](./images/delete.svg) button\n\n 5. Click on the **OK** button to confirm\n\n
    \n\n\n## Overlay Properties\n\n### Overlay Name\n\nThe name is a single line text field that supports unicode characters.\n\n
    \n\n To 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 ![Overlays](./images/layers.svg) 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### Overlay Visibility\n\nOverlays are visible on the image by default once attached.\n\n
    \n\n To 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 ![Overlays](./images/layers.svg) button in the left sidebar\n\n 3. Identify the overlay entry to be modified\n\n 4. Click on the ![Eye](./images/eye.svg) button to toggle visibility\n\n
    \n\n
    \n\n To 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 ![Overlays](./images/layers.svg) button in the left sidebar\n\n 3. Click on the ![Eye](./images/eye.svg) button at the top right corner of the Overlays panel to toggle visibility for all overlays\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\n
    \n\n To 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 ![Overlays](./images/layers.svg) button in the left sidebar\n\n 3. Click on the ![Show Transformation](./images/transform.svg) 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 ![Scale to Fit](./images/scale-to-fit.svg) 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 Transform is available for manually created overlays but not for overlays that have been imported from image analysis systems.\n
    \n\n
    \n\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\n
    \n\n To 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 ![Overlays](./images/layers.svg) 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\n To 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 ![Overlays](./images/layers.svg) 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\n To 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 ![Overlays](./images/layers.svg) 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 To 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 ![Overlays](./images/layers.svg) button in the left sidebar\n\n 3. Select a composite mode from the dropdown 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### 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\n
    \n\n Overlay 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","slug":"docs/viewer/overlays"},{"frontmatter":{"title":"Split View","description":"split view"},"rawBody":"---\ntitle: Split View\ndescription: split view\norder: 23\nsection: Viewer\n---\n\n\n# Split View\n\n
    \n\nSplit View allows multiple images to be viewed 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\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\n To launch Split View from the Repository \n\n 1. Navigate to any folder in the Repository (click on the ![Folder](./images/repository-folder.svg) **Repository** button from the left-hand sidebar 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. Right-click on the item (or items) to bring up the context menu\n\n 4. Click on **View Images**\n\n
    \n\n
    \n\n To launch Split View from Search \n\n 1. Perform a search (click on the ![Search](./images/repository-search.svg) **Search** button from the left-hand sidebar 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. Right-click on the item (or items) to bring up the context menu\n\n 4. Click on **View Images**\n\n
    \n\n
    \n\n To 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 ![Folder](./images/folder.svg) 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 the item (or items) to bring up the context menu\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\n To 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 ![Folder](./images/folder.svg) 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## 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\n
    \n\n To change the number of rows or columns \n\n 1. Click on the ![Layout](./images/viewer-layout.svg) 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 bottom of 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 right side of 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\n To 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 ![Expand Toolbar](./images/expand.svg) button to expand the toolbar if necessary\n\n 3. Click on the ![More](./images/more.svg) 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\n To 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 ![Expand Toolbar](./images/expand.svg) button to expand the toolbar if necessary\n\n 3. Click on the ![More](./images/more.svg) 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\n To 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 ![Expand Toolbar](./images/expand.svg) button to expand the toolbar if necessary\n\n 3. Click on the ![More](./images/more.svg) menu\n\n 4. Select **Remove Row** or **Remove Column** from the dropdown menu\n\n
    \n\n
    \n\n To move an image panel \n\n 1. Hover or click on the image you want to move\n\n 2. Click on the ![Move](./images/move.svg) handle at the top right corner of the image and drag it to the new location\n\n
    \n\n
    \n\n To 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 ![Resize](./images/viewer-resize-handle.svg) 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### 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\n
    \n\n To change the aspect ratio of panels \n\n 1. Click on the ![Layout](./images/viewer-layout.svg) 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
    \n\n
    \n\n\n### Panel Spacing\n\nThe spacing between each panel (i.e. the separation between panels) can be customized.\n\n
    \n\n To change the spacing between panels \n\n 1. Click on the ![Layout](./images/viewer-layout.svg) 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\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\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 grey dot in the Browse Folder Panel.\n
    \n\n
    \n\n To 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\n To view the slide label for a panel \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. Hover over the ![Info](./images/toolbar-info.svg) icon in the toolbar to see the slide label for that image\n\n
    \n\n
    \n\n To 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 ![Expand Toolbar](./images/expand.svg) button to expand the toolbar if necessary\n\n 3. Click on the ![Rotate](./images/rotate.svg) button in the toolbar to show or hide the rotation tool\n\n
    \n\n
    \n\n To add an image to an empty panel \n\n 1. Click on the **Add a slide** button in the center of an empty panel\n\n 2. In the **Select Cell Slide** 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### 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\n
    \n\n To 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 ![Expand Toolbar](./images/expand.svg) button to expand the toolbar if necessary\n\n 3. Click on the ![Palette](./images/palette.svg) button dropdown 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## Panel Contents\n\n
    \n\n To 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 ![Expand Toolbar](./images/expand.svg) button to expand the toolbar if necessary\n\n 3. Click on the ![More](./images/more.svg) 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 To 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 ![Expand Toolbar](./images/expand.svg) button to expand the toolbar if necessary\n\n 3. Click on the ![More](./images/more.svg) menu\n\n 4. Select **Change Slide** from the dropdown menu\n\n 5. In the **Select Cell Slide** 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## 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\n
    \n\n To 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 ![Folder](./images/folder.svg) 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 To 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 ![Expand Toolbar](./images/expand.svg) button to expand the toolbar if necessary\n\n 3. Click on the ![More](./images/more.svg) 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
    \n\n
    \n\n
    \n\n To 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 ![Expand Toolbar](./images/expand.svg) button to expand the toolbar if necessary\n\n 3. Click on the ![Fill View](./images/fill-view.svg) button\n\n
    \n\n
    \n\n To 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 ![Expand Toolbar](./images/expand.svg) button to expand the toolbar if necessary\n\n 3. Click on the ![Shrink View](./images/shrink-view.svg) button\n\n
    \n\n
    \n\n To 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 ![Folder](./images/folder.svg) 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 Slide** dialog that pops up, click on the **Yes** button\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\n
    \n\n To 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 ![Lock](./images/lock.svg) button\n\n 3. Repeat steps 1 and 2 for each image to synchronize\n\n
    \n\n
    \n\n To 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 ![Down Arrow](./images/down-arrow.svg) button next to the ![Lock](./images/lock.svg) button\n\n 3. Select **Synchronize Row** or **Synchronize Column** from the dropdown menu\n\n
    \n\n
    \n\n To synchronize all images in the Viewer \n\n 1. Click on the ![Lock](./images/lock.svg) button in the Viewer top bar to display the synchronize menu\n\n 2. Select **Synchronize All** from the dropdown menu\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\n
    \n\n To 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 To 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## 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\n
    \n\n To 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 ![Folder](./images/folder.svg) 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 Slide** dialog that pops up, click on the **Yes** button\n\n
    \n\n
    \n\n To 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 ![Folder](./images/folder.svg) 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
    \n\n To replace the Viewer content with multiple images 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 ![Folder](./images/folder.svg) 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 Viewer\n\n 5. In the **Placement** dialog that pops up, select **Replace View**\n\n 6. Select the desired layout from the dropdown menu\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 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","slug":"docs/viewer/split-view"}]},"site":{"siteMetadata":{"showSearch":true,"showVersions":true}}}}