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. 

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

Opening caMicroscope

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 which database of images you want to view by clicking either the large slide image or the More button. Databases include Breast Cancer Genomic Pilot, Virtual Tissue Repository (VTR) Pending, and Pancreatic Ductal Adenocarcinoma (PDAC).
   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.

   To select a different image, click the Back button in your browser to return to the table.

Using the caMicroscope Toolbar

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.

To Zoom In: Click in the main window.

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.

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.
3. Click your mouse to control the bounding box and drag it up, down, left, and right to see different parts of the main content window.

Filtering Markups

You can filter your view of the markups on the images in caMicroscope by an area based on one or more selected algorithms. The algorithms available in caMicroscope have been run against the full set of images.

To filter markups

1. Click the Filter Markups button.
   The Select Algorithm box appears.
2. Click the box to the left of each algorithm you want to select.
   caMicroscope runs the algorithm(s) against each image in the dataset. This can take some time. The markups appear in the color noted in the Select Algorithm box. You may have to zoom in and pan the image to see all markups.

Analyzing Images

To analyze images

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 .