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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. It also allows you to view and analyze nuclear segmentations of images.Â
This guide explains how to do the following tasks in caMicroscope:
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- Use the Chrome browser to navigate to https://wolf.cci.emory.edu/vtr_pending. Â
The Sign In to caMicroscope.ÂThe Login page appears.
SEER VTR caMicroscope Login Page Use your Google credentials to sign in to caMicroscope.
The caMicroscope site appears.
caMicroscope Home Page- 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, or and Pancreatic Ductal Adenocarcinoma (PDAC) caMicroscope database of images by clicking either the large slide image or the More button.Â
A table appears that lists all whole-slide images for the selected database that you are authorized to view.
caMicroscope Data Table for the PDAC Database In the table, click the the Open button  button for any row.
The slide opens in caMicroscope.Note To select a different image, click the Back button in the caMicroscope toolbar or the back arrow in your browser to return to the table.
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Panning allows you to move the image inside the window.
- Select an image and view it in caMicroscope. See Opening caMicroscope for more information.
- 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 - Drag Click your mouse to control the bounding box and drag it up, down, left, and right to see different parts of the main content windowalong 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
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- towards the plus sign.Â
- 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 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
Tool | Name | Purpose | |||||||
Annotations | Opens the Annotations Annotation panel, where you can select which annotation set to view, name that annotation set, add optional notes about the annotation set, save itthe annotation set, and reset the panel to its original state.
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Layer Manager | Opens the Layers Manager panel, where you can select which layers to view. | ||||||||
Home | Return to the data table so that you can open another slide. | ||||||||
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 | The 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 | Drag this tool on the slide to learn the measurement in micrometers.
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Share View | Opens 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 | 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.
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Heat MapHeatmap | 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 A plot of cross-tabulated feature correlations appears. The heat map shown in the cross-tabulation is a sampling of over a million segmented objects in the dataset. Hover your mouse over the colored pixels in the feature correlations. Each pixel is a single segmented object. The features that intersect at each pixel are highlighted in yellow, the intersected pixel is outlined in orange and filled with an X, and the feature names appear in a popup window.The colors in the heat map show how high or low the correlations between intersecting features are. The orange shows the pixels of the highest correlation. The orange diagonal line shows where features are identical on both axes. . Choices of heatmaps: HeatMap displaying a gradient for lym: Slides with heatmaps have three custom tools in the toolbar.
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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.
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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
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Help | Opens this guide | Labeling | Segment | Bug Report | Opens a Google Form where you can describe the issue you have experienced. | ||||
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. |