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SEER VTR (Surveillance, Epidemiology, and End Results Virtual Tissue Repository) 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:

Table of Contents

Opening caMicroscope

  1. Use the Chrome browser to navigate to caMicroscope. 

    The Login 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.
    SEER VTR caMicroscope Login Page

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

    caMicroscope Home Page

  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
    caMicroscope Data Table for the PDAC Database

  4. In the table, click the Open button for any row.
    The slide opens in caMicroscope.

    Note

    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. See SEER VTR Opening caMicroscope User Guide for more information.
  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.

    caMicroscope Main Content Window and Inset 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.

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Inset window showing the zoom slider and a red bounding box around the entire slide.
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.

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