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PathcoreFlow User Manual

Figure Maker

[add-on]

Figure Maker extends the capabilities of Split View for creating publication-ready Figures. Using Figure Maker it's possible to decorate image panels created with 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:

  • Save image panels created with Split View
  • Add markup such as scale bars, text labels, and slide labels to image panels
  • Easily configure the visibility of annotations and image overlays
  • Export image panels in common image formats

Creating a Figure

Figures are created when image panels, that are created using 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.

When 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.

If you attempt to modify an item which is governed by a reason for change tracking policy, you will be required to provide a reason for the change.
To create a Figure from within the Viewer

  1. Open one or more images in the Viewer to create image panel(s). See Split View for more details

  2. (Optional) Configure the markup for the panel(s). See Figure Markup for more details

  3. Click on the Menu icon at the right corner of the Viewer top bar

  4. Select Save As from the dropdown menu

  5. In the Save As dialog that pops up, navigate to a folder using the folder browser

    • Click on the folder name dropdown at the top of the dialog to see a list of folders related to the current view, and a list of recently visited folders

  6. Enter a Name in the text box at the bottom left

  7. Click on the Save button

Changes that affect the appearance of image panel(s) are saved, including the panel layout, ROI, and markup.
To save changes made to a Figure

  1. Make changes to the Figure, such as adding annotations and labels. See Figure Markup for more details

  2. Click on the Menu icon at the right corner of the Viewer top bar

  3. Select Save from the dropdown menu

Changes that affect the appearance of image panel(s) are saved, including the panel layout, ROI, and markup.
To open a previously saved Figure

  1. Navigate to any folder in the Repository (click on the Folder Repository button from the Navigation Menu then navigate to a folder)

  2. Click on an item with the Figure icon or that has the Type of "Figure" in the file listing

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).
To rename a Figure from within the Viewer

  1. Click on the Edit icon next to the current name of the Figure at the top left of the Viewer (defaults to "Untitled View")

  2. Type the new name for the Figure

To rename a Figure from the Repository

  1. Navigate to any folder in the Repository (click on the Folder Repository button from the Navigation Menu then navigate to a folder)

  2. Right click on an item with the Figure icon or that has the Type of "Figure" in the file listing to bring up the context menu

  3. Click Rename

  4. In the popup dialog, type a new name for the Figure

  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

Figure Markup

Many 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.

Image Annotations

The 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.

Annotations can only be created when annotations on the panel are visible.
To toggle the visibility of annotations on an image panel

  1. Hover or click on the image to reveal the toolbar at the top left of the panel

  2. Click on the Expand Toolbar button to expand the toolbar if necessary

  3. Click on the Pen button to reveal the markup menu

  4. Adjust the Annotations toggle to show or hide image annotations

  5. (Optional) Click on Annotations to expand the section and click on Apply to All Slides to apply the visibility setting to all panels

Borders of snapshots are not included in exported Figures even when annotations are visible.
To create annotations on an image panel

  1. Ensure annotations for the image panel are visible (see above)

  2. Right-click on the image to open up the annotation ring

  3. Select an annotation tool and follow the on-screen instructions to create a new annotation. See Creating Annotations for more details

Slide Label

The slide label can be overlaid on an image panel and made visible until it's removed.

To toggle the visibility of the slide label on an image panel

  1. Hover or click on the image to reveal the toolbar at the top left of the panel

  2. Click on the Expand Toolbar button to expand the toolbar if necessary

  3. Click on the Pen button to reveal the markup menu

  4. Adjust the Slide Label toggle to show or hide the label

  5. Click on Slide Label to expand the section and adjust preferences

    1. (Optional) Adjust the location of the label by clicking one of the four corners in the control to the right of Alignment
    2. (Optional) Click on the Rotate button to rotate the label
    3. (Optional) Click on Apply to All Slides to apply these settings to all panels

Text Label

A text label can be overlaid on an image panel and made visible until it’s removed.

To include a text label on an image panel

  1. Hover or click on the image to reveal the toolbar at the top left of the panel

  2. Click on the Expand Toolbar button to expand the toolbar if necessary

  3. Click on the Pen button to reveal the markup menu

  4. Adjust the Label toggle to show or hide the label

  5. Click on Label to expand the section and adjust preferences

    1. (Optional) Adjust the label text in the field below the toggle (default text will be the image name)
    2. (Optional) Adjust the location of the label by clicking one of the four corners in the control to the right of Alignment
    3. (Optional) Adjust the text color by clicking in the colored box to the right of Foreground, then selecting a color
    4. (Optional) Adjust the text background color by clicking in the colored box to the right of Background, then selecting a color
    5. (Optional) Click on Apply to All Slides to apply these settings to all panels

Scale Bar

A scale bar can be overlaid on an image panel and made visible until it’s removed.

To include a scale bar on an image panel

  1. Hover or click on the image to reveal the toolbar at the top left of the panel

  2. Click on the Expand Toolbar button to expand the toolbar if necessary

  3. Click on the Pen button to reveal the markup menu

  4. Adjust the Scale Bar toggle to show or hide the scale bar

  5. Click on Scale Bar to expand the section and adjust preferences

    1. (Optional) Adjust the location of the scale bar by clicking one of the four corners in the control to the right of Alignment
    2. (Optional) Adjust the text and scale bar color by clicking in the colored box to the right of Color, then selecting a color
    3. (Optional) Adjust the Show measurement text toggle to show or hide the measurement
    4. (Optional) Adjust the Show border toggle to show or hide a border around the text and scale bar
    5. (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
    6. (Optional) Select the location of the measurement text relative to the scale bar by clicking one of the Text Alignment options: Align Left (left), Align Center (center), or Align Right (right)
    7. (Optional) Click on Apply to All Slides to apply these settings to all panels

Downloading Figures

The contents of a Figure can be exported as a common image format (PNG, JPEG, TIFF, or PDF) for use in presentations or other documents.

To export a Figure from the Repository

  1. Navigate to any folder in the Repository (click on the Folder Repository button from the Navigation Menu then navigate to a folder)

  2. Select a Figure object from the folder listing

  3. Bring up the context menu for the item

  4. Click on Export figure to bring up the Download Figure popup dialog

  5. Click on the Download menu at the bottom right of the dialog

  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 in the exported image

  7. Click on the Download button

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

To export a Figure from within the Viewer

  1. Create a new Figure or open an existing Figure in the Viewer

  2. Click on the Camera button in the Viewer top bar to display the Download dialog

  3. 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 in the exported image

  4. Click on the Download button

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

Deleting Figures

Figures can be deleted from the Repository or from within the Viewer.

To delete a Figure from the Repository

  1. Navigate to any folder in the Repository (click on the Folder Repository button from the Navigation Menu then navigate to a folder)

  2. Select a Figure object from the folder listing

  3. Bring up the context menu for the item

  4. Click on Delete

  5. Click on the Yes button to confirm

To delete a Figure from within the Viewer

  1. Open the Figure in the Viewer

  2. Click on the Menu icon at the right corner of the Viewer top bar

  3. Select Delete Figure from the dropdown menu

  4. Click on the Yes button to confirm