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- Use the Chrome browser to navigate to https://wolf.cci.emory.edu/vtr_pending. caMicroscope.
The Sign In page appears.
- Use your Google credentials to sign in to caMicroscope.
The caMicroscope site appears. - Select the Breast Cancer Genomic Pilot, Virtual Tissue Repository (VTR) Pending Slides, or Pancreatic Ductal Adenocarcinoma (PDAC) caMicroscope database of images by clicking either the large slide image or the More button.
A table appears that lists all whole-slide images for the selected database that you are authorized to view.
In the table, click the Open button for any row.
The slide opens in caMicroscope.Note To select a different image, click the Back button in your browser to return to the table.
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- Select an image and view it in caMicroscope.
- In the inset window, note the red bounding box. This bounding box is your view of the current image in the main content window.
Click - Drag 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.
- 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.
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Tool | Name | Purpose |
| 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 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. |
| Heat Map | 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. REVIEW BELOW TEXT: 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. |
| 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. You are prompted to confirm this change. |
