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PathcoreScholar User Manual

Snapshots


Snapshots 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.

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.

Creating Snapshots

Use 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 and from the Metadata tab in the Folder Listing.

To create a snapshot

  1. From within the Viewer, right-click on an image to open up the annotation ring

  2. Select the Snapshot tool

  3. Hold and drag the frame to capture a region of interest

  4. (Optional) In the popup dialog, click on the first line of text (default: “Untitled Snapshot”) and provide a name for the snapshot

  5. (Optional) In the popup dialog, click on the second line of text (default: “No description”) and provide a description for the snapshot

The bounding box of a snapshot cannot be edited after it has been drawn.
To navigate to an existing snapshot

  1. If the left sidebar is not displayed, toggle it by clicking on the Menu > button at the bottom left of the Viewer

  2. Hover or click on the Info button in the left sidebar

  3. Scroll down to the Snapshots section

  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

Downloading Snapshots

The 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.

To download a snapshot from within the Viewer

  1. From within the Viewer, locate the snapshot on the image

  2. Click on the snapshot title to reveal a dialog

  3. Click on the Download button in the popup dialog

  4. Adjust preferences

    1. (Optional) Show/hide image annotations via the show annotations toggle
    2. (Optional) Enable the show label toggle to reveal a text overlay
    3. (Optional) Enable the show scale bar toggle to reveal a scale bar

  5. Click on the Download menu

  6. Adjust preferences such as

    • Size: adjust the width or height to specify the desired size
    • File type: select the desired format from the dropdown
    • White Background: Enable to use a white background instead of the default black

  7. Click on the Download button

  8. If prompted, select a location to save the downloaded file

To download a snapshot from the Information panel

  1. If the left sidebar is not displayed, toggle it by clicking on the Menu > button at the bottom left of the Viewer

  2. Hover or click on the Info button in the left sidebar

  3. Scroll down to the Snapshots section

  4. Select a snapshot by clicking on its thumbnail to reveal more options

  5. Click on the Download button

  6. Adjust preferences

    1. (Optional) Show/hide image annotations via the show annotations toggle
    2. (Optional) Enable the show label toggle to reveal a text overlay
    3. (Optional) Enable the show scale bar toggle to reveal a scale bar

  7. Click on the Download menu

  8. Adjust preferences such as

    • Size: adjust the width or height to specify the desired size
    • File type: select the desired format from the dropdown
    • White Background: Enable to use a white background instead of the default black

  9. Click on the Download button

  10. If prompted, select a location to save the downloaded file

Snapshot Markup

When 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.

To include image annotations on a downloaded snapshot

  1. Enable the Show annotations toggle in the snapshot download dialog (all annotations visible on the image will be included)

  2. To hide some annotations, ensure they are hidden prior to launching the download dialog

To include a label on a downloaded snapshot

  1. Enable the Show label toggle in the snapshot download dialog

  2. (Optional) Adjust the label text in the field below the toggle (default text will be the image name)

  3. (Optional) Adjust the location of the label by clicking one of the four corners in the control to the left of Alignment

  4. (Optional) Adjust the text color by clicking in the colored box to the left of Foreground, then selecting a color

  5. (Optional) Adjust the text background color by clicking in the colored box to the left of Background, then selecting a color

To include a scale bar on a downloaded snapshot

  1. Enable the Show scale bar toggle in the snapshot download dialog

  2. (Optional) Adjust the location of the scale bar by clicking one of the four corners in the control to the left of Alignment

  3. (Optional) Adjust the text and scale bar color by clicking in the colored box to the left of Foreground, then selecting a color

  4. (Optional) Adjust the Show measurement text toggle to show or hide the measurement

  5. (Optional) Adjust the Show border toggle to show or hide a border around the text and scale bar

  6. (Optional) Adjust the Automatic length toggle to determine the size of the scale bar

    • When enabled the size is determined automatically
    • When disabled the user can specify the size of the scale bar and select a unit of measurement from the dropdown

  7. (Optional) Select the location of the measurement text relative to the scale bar from the Text Alignment dropdown (auto, left, center, or right)

Snapshot Properties

Snapshot Name

The 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.

To rename a snapshot from within the Viewer

  1. From within the Viewer, locate the snapshot on the image

  2. Click on the snapshot title to reveal a dialog

  3. Click on the first line of text in the popup dialog (default: “Untitled Snapshot”)

  4. Provide a name or edit the existing text

  5. Press the Enter key or click away from the textbox to save your changes

To rename a snapshot from the Information panel

  1. If the left sidebar is not displayed, toggle it by clicking on the Menu > button at the bottom left of the Viewer

  2. Hover or click on the Info button in the left sidebar

  3. Scroll down to the Snapshots section

  4. Select a snapshot by clicking on its thumbnail to reveal more options

  5. Click on the Rename button

  6. Provide a name or edit the existing text in the popup dialog

  7. Click on the Rename button or press the Enter key to save your changes

Snapshot Description

The 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.

To change the description of a snapshot from within the Viewer

  1. From within the Viewer, locate the snapshot on the image

  2. Click on the snapshot title to reveal a dialog

  3. Click on the second line of text in the popup dialog (default: “No description”)

  4. Provide a description or edit the existing text

  5. Press the Enter key or click away from the textbox to save your changes

Snapshot Visibility

Snapshots are visible on the image by default once created. If you need to declutter the image, you may hide all snapshots at once.

To change the visibility of all snapshots

  1. If the left sidebar is not displayed, toggle it by clicking on the Menu > button at the bottom left of the Viewer

  2. Hover or click on the Info button in the left sidebar

  3. Scroll down to the Snapshots section

  4. Click on the Eye button, adjacent to the Snapshots title, to toggle visibility for all snapshots

Deleting Snapshots

Snapshots can be deleted from within the Viewer or from the Information panel.

To delete a snapshot from within the Viewer

  1. From within the Viewer, locate the snapshot on the image

  2. Click on the snapshot title to reveal a dialog

  3. Click on the Download button in the popup dialog

  4. Click on the OK button to confirm

To delete a snapshot from the Information panel

  1. If the left sidebar is not displayed, toggle it by clicking on the Menu > button at the bottom left of the Viewer

  2. Hover or click on the Info button in the left sidebar

  3. Scroll down to the Snapshots section

  4. Select a snapshot by clicking on its thumbnail to reveal more options

  5. Click on the Delete button

  6. Click on the Yes button to confirm