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caMicroscope caMicroscope is a digital pathology data management, visualization, and analysis platform. It tool to view, annotate, and analyze biomedical images. It consists of a set of web services to manage 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. caMicroscope hosts whole-slide, pancreatic cancer tissue images for review by pathologists.
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caMicroscope allows you to view whole slide images and nuclear segmentations.
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Opening caMicroscope
- Use the Chrome browser to navigate to httphttps://quip3wolf.bmicci.stonybrookemory.edu/vtr_pending.
The Sign In page appears. - Use your Google credentials to sign in to caMicroscope.
The caMicroscope site appears.
Viewing Images
- Log in to caMicroscope and click the icon for the caMicroscope toolSelect 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. - In the table, click the Open button for any row.
caMicroscope, a web-based pathology viewer, opensThe 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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The following buttons on the toolbar launch features described in this guide.
Tool | Name | Purpose |
Home | Return to the caMicroscope home page. | |
Lymphocyte & Plasma Cell App | Launch the Lymphocyte & Plasma Cell App within caMicroscope. For more information, see page 6. | |
Segment Curation App | Launch the Segment Curation App within caMicroscope. For more information, see page 7. | |
Filter Markups | View only those markups associated with selected algorithms. For more information, see page 8. | |
Image Analysis | Not yet available. |
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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The following tools are available on the toolbar.
Tool | Name | Purpose |
Home | Return to the caMicroscope home page | |
caMicroscope | Return to the caMicroscope application | |
Filter Markups | View only those markups associated with selected algorithms. For more information, see page 8. | |
Show/Hide Markups | View the image with or without markups. | |
Decrease Opacity | Decrease the opacity of the selected markup(s), making it/them more transparent. | |
Increase Opacity | Increase the opacity of the selected markup(s), making it/them less transparent. | |
Show Weight Panel | This panel allows you to adjust the automatic lymphocyte prediction results for this slide, with the options described below.
Adjust the sensitivity of lymphocyte prediction. Choose a higher volume for more predicted lymphocyte regions.
Adjust the specificity of necrosis prediction. Choose a higher volume for more predicted lymphocyte regions.
Show lymphocyte prediction without necrosis filtering.
Show necrosis prediction.
Show lymphocyte prediction with necrosis filtering (recommended). | |
Free Line Markup | Draw thin lines, thick lines, or polygons on the image. | |
Switch User | If you are a super user, click this button to review and change other people’s annotations. |
Using the Segment Curation App
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The Segment Curation App has the following tools.
Tool | Name | Purpose |
Home | Return to the caMicroscope home page. | |
Free Line Markup | Draw thin lines, thick lines, or polygons on the image. | |
Save ViewPort | For a selected algorithm, save the ViewPort. | |
Save Rectangle and Delete Annotations in This Area | For an area based on a selected algorithm, save the rectangle and delete the annotations. | |
Filter Markups | View only those markups associated with selected algorithms. For more information, see page 8. | |
Generate Composite Dataset |
ColorMap |
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.
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