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1. Use the Chrome browser to navigate to https://wolf.cci.emory.edu/vtr_pending.  
   The Sign In page appears.
   
   
2. Use your Google credentials to sign in to caMicroscope.
   The caMicroscope site appears.
3. 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.

4. 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.

Using the caMicroscope

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Tools

Use the toolbar buttons to manipulate the slide.

Zooming In and Out

To zoom in on the image, click the main content window with your mouse. Each time you click, the view zooms in further, the scale updates, and the bounding box in the inset window changes to show how much of the total image is in the main content window. When you are zoomed in very far, the bounding box may not be visible. Zooming out reverses this process.

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To Zoom Out: Press and hold the Shift key while you click on the main window.

Zoomed in:

Zoomed out:

Panning an Image

Panning allows you to move the image inside the window.

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1. Log in to caMicroscope and then click the icon for FeatureScape.
   
   The SlideSelect page appears.
2. From the drop-down list, select an analysis set containing images you want to view and explore. The analysis sets are analyses that have been run on the entire dataset. The diagnostic images within an analysis set have been analyzed with the algorithm named in the analysis set.
3. Click a link in the caMicroscope column to view the diagnostic image in caMicroscope.
4. Click the Explore Features button in the row of an image you want to explore.
   
   A plot of cross-tabulated feature correlations appears.
   
   NOTE: The heat map shown in the cross-tabulation is a sampling of over a million segmented objects in the dataset.
5. 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.
   
   NOTE: The colors in the heat map show how high or low the correlations between intersecting features are. The orange shows the pixels of highest correlation. The orange diagonal line shows where features are identical on both axes.

Selecting a Region on the Scatterplot

Select a region on the scatterplot to zoom in to a subset of segmented objects.

To select a region:

1. Move your cursor over the scatterplot to see the crosshairs.
2. Click an area of interest and drag your cursor to create a rectangle.
3. Release the mouse. The scatterplot zooms in to the selection.

You can now view nuclear mugshots or download data from the selected region. To return to the original scatterplot, click the selected pixel in the heat map again.

Viewing Nuclear Mugshots

Nuclear mugshots are screenshots of segmented nuclei in the set of features you selected in the heat map. Only a sampling of the millions of images has associated mugshots.

To view nuclear mugshots:

1. Select an area of interest on the scatterplot.
2. Click Nuclear mugshots from selected region.
   The nuclear segmentation viewer opens, showing tiles of slides that match the range you selected.
3. Click any tile to open it in caMicroscope and view it in the context of the whole slide image.
   NOTE: Make sure you are logged into caMicroscope before you select a tile.

Downloading Data from a Scatterplot

To download data from a scatterplot

1. Select an area of interest on the scatterplot.
2. Click .
   The FeatureScape Data Download page appears.
3. Review the information on the page to confirm the relative time it will take to download your selection.
4. Enter the maximum number of features to download and then click .
   The Data Download page refreshes with a list of variables represented in the download. You can select some or all of them and then click .