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caMicroscope is a tool to view, annotate, and analyze whole-slide, biomedical images. It manages digital pathology images, associated clinical and imaging metadata, and human/machine generated annotations and markups.

This guide explains how to do the following tasks in caMicroscope:

Opening caMicroscope

  1. Use the Chrome browser to navigate to caMicroscope. 

    The Login page appears.

    SEER VTR Microscope login window showing a Log in with Google option and a username and password option, Don't remember your password link, and a log in button. A Sign Up tab is grayed out.
    SEER VTR caMicroscope Login Page

  2. Use your Google credentials to sign in to caMicroscope.
    The caMicroscope site appears.

    caMicroscope Home Page

  3. Select one of the image databases by clicking either the large slide image or the More button. Options include the Breast Cancer Genomic Pilot, Virtual Tissue Repository (VTR) Pending Slides, and Pancreatic Ductal Adenocarcinoma (PDAC).
    A table appears that lists all whole-slide images for the selected database that you are authorized to view.

    caMicroscope slide table for the PDAC database
    caMicroscope Data Table for the PDAC Database

  4. In the table, click the Open button for any row.
    The slide opens in caMicroscope.

    To select a different image, click Home button in the caMicroscope toolbar or the back arrow in your browser to return to the table.

Panning the Slide

Panning allows you to move the image inside the window.

  1. Select an image and view it in caMicroscope. See Opening caMicroscope for more information.
  2. In the inset window, note the red bounding box. This bounding box is your view of the current image in the main content window.

    caMicroscope Main Content Window and Inset Window
  3. Drag your mouse along the main content window.
    The red bounding box moves to reflect your current position.

Zooming In and Out

The inset window has a zoom slider above it.

  • To zoom in on the image, move the slider towards the plus sign. 
  • To zoom out, move the slider in the inset window towards the minus sign.

As the slider moves, the main content window zooms in or out and the red bounding box in the inset window changes to show how much of the total image is in the main content window.

Inset window showing the zoom slider and a red bounding box around the entire slide.
Inset Window with Red Bounding Box and Zoom Slider

Using the caMicroscope Tools

The toolbar is in the top-left of the main content window. Use the toolbar buttons to manipulate the slide. To close any toolbar button, click the same button again or a new button.

caMicroscope toolbar with buttons as described in the following table.
caMicroscope Toolbar

Tool

Name

Purpose

Annotations button

Annotations

Opens the Annotation panel, where you can select which annotation set to view, name that annotation set, add optional notes about the annotation set, save the annotation set, and reset the panel to its original state.

Annotation panel showing AnnotSchema open, an Identity Name text box, a Notes field, Reset button, and Save button
Annotation Panel

Layer Manager button

Layer Manager

Opens the Layers Manager panel, where you can select which layers to view.

Home button

Home

Return to the data table so that you can open another slide.

Draw button

Draw

Draw thin lines, thick lines, or polygons on the image. To maintain the integrity of measurements, avoid drawing shapes that overlap or intersect one another.

Magnifier button

MagnifierThe Magnifier works like a magnifying glass and allows you to see the slide at normal magnification (1.0), low magnification (0.5), or high magnification (2.0). Click a magnification level and place the bounding box on the area of the slide you want to magnify.

Measurement button

Measurement

Drag this tool on the slide to learn the measurement in micrometers.

An portion of a slide showing a measurement of 3.373 micrometers. A line separates the start and end points of the measurement.
Small Area of One Slide

Share View button

Share ViewOpens a window with a URL to the current presentation state of the slide including the magnification level, layers that are currently open, and your position on the image.

Side by side viewer button

Side by Side Viewer

Shows the Layer Manager panel, the left and right layers, and inset window. For the right and left layer, select which layer you want to view.

Three panels in caMicroscope that include the Layer Manager panel, the left and right layers. Also shows the inset window in the lower right corner.
Side-by-Side Viewer

Heatmap tool button

Heatmap

For a slide with heatmap data, opens the choices of heatmaps available, as well as ways of displaying the heatmaps. The gradient shows all of the values on the selected spectrum for the field you selected.

Choices of heatmaps:

HeatMap List window, showing links for lym_v1-high_res and lym_v1-low_res

HeatMap displaying a gradient for lym:

Slide showing a heat map on top of the original slide image. A shorter toolbar is at the top left that is customized for use with heat maps and described in this table.

Slides with heatmaps have three custom tools in the toolbar.

  • Edited Data List tool button Opens the Edited Data List. Information appears here if the slide has been edited using the HeatMap Editor tool, described below.
  • Heatmap settings tool buttonOpens the Heatmap Settings window, where you can turn the gradient display on and off and adjust the property of the gradient. By default, both lymphocyte and necrosis concentrations appear in the heatmap.

    • If you choose to turn the gradient display on by clicking the checkbox, you can choose to display either the lymphocyte or necrosis heatmap by itself.
    • If you display the lymphocyte gradient, you can set its property between 0 and 1.
    • If you display the necrosis gradient, its property is fixed at 1.
  • HeatMap Editor tool button Opens the HeatMap Editor.

    Select an operation from the list. Each edits the heatmap to show that operation, lym-positive, lym-negative, necrosis-positive, and necrosis-negative, in the specified color.

Labeling tool button

Labeling

Use this tool to draw a circle or rectangle around a tumor region, measure an area on the slide, download labels, and submit a bug report. The Labeling tool has its own toolbar with tools in the following order from left to right: return to the previous slide, place a square on the slide, place a circle on the slide, measure an area, download labels, and submit a bug report. Click the left arrow at the far right of the toolbar to hide it, then click the right arrow to show it.

Labeling toolbar with icons that have the functions described in the previous sentence.
Labeling Toolbar

  • Previous slide tool button Returns you to the previous slide.
  • Allows you to place a square-shaped annotation () on the slide to emphasize one block of the heatmap. Hover your mouse over the X icon to show an edit button Edit button, which you click to provide notes about your annotation. Hover your mouse over the square annotation to open a color picker you can use to change the color of the square.
  • Draw Circle tool button Allows you to place a circle annotation () on the slide to emphasize one block of the heatmap. Hover your mouse over the X icon to show an edit button Edit button, which you click to provide notes about your annotation. Hover your mouse over the circle annotation to open a color picker you can use to change the color of the circle.
  • Measures an area you select on the slide in micrometers.
  • Download labeling button Allows you to download the labels you've added to annotations. The file you download is a zip file that includes JPG and CSV files.
  • Bug report button Allows you to log a bug in a Google Form.

Segment tool button

Segment

This tool allows you to display, count, and export nuclear segmentations on the image. Clicking this tool opens the following custom toolbar.

Segment Toobar

  • Click the Segment tool to open the custom toolbar above. Then click the Segment tool again, place your cursor on the image, and select a rectangular area. The Segment tool opens another custom toolbar, which follows, and counts the number of segmented objects in the selected area.

    Segment object toolbar, which contains tools for saving
    Segment Object Toolbar

    On the Segment Object toolbar, you can do the following tasks.

    • Click Close tool button, which is a black X on a white background to close the Segment Object toolbar.
    • Click Save as ROI (region of interest) Image button to save the segmented objects in the selected area as a Region of Interest (ROI) image file. The file downloads to your default download location.
    • Click to save the segmented objects in the selected area to a Comma-Separated Values (CSV) file. Column headers include AreaInPixels, PerimeterInPixels, and Polygon. The file downloads to your default download location.
    • Click to open the segmentation settings.
      Segmentation Settings toolbar, which allows you to adjust the max area, min area, and threshold
      Segmentation Settings Options
      • Settings you can customize for the segmented area include max area, min area, and threshold. Select objects by dragging the slider.
  • Previous slide tool buttonReturns you to the previous slide.
  • Bug report button Allows you to log a bug in a Google Form.

Question mark icon for online help access

HelpOpens this guide.

Reviewed button

Reviewed

Click this button after reviewing a slide to change its review status, then confirm the change. A green checkmark appears in the data table for this slide after you have marked it as reviewed.

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