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

  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

  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.
  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.
    Image of slide in caMicroscope showing a breast cancer image in the main content window and an inset window that shows the same image with a red box around it, indicating that the full slide image is being shown in the main content 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.

Using the caMicroscope Tools

Use the toolbar buttons to manipulate the slide. To close any toolbar button, click the same button again or a new button.

Tool

Name

Purpose

Annotations button

Annotations

Opens the Annotations 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

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.

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 ViewerShows 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.

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.

ToolDescription
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 button

Opens 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 buttonOpens 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.

ToolDescription
Previous slide tool buttonReturns 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 buttonAllows 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 buttonAllows 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 buttonAllows you to log a bug in a Google Form.


Segment tool button

Segment

Bug report button

Bug ReportOpens a Google Form where you can describe the issue you have experienced.

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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