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Page History
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Tool | Name | Purpose |
| Annotations | Opens the Annotations panel, where you can |
| Layer Manager | |
| Home | Return to the caMicroscope home page. |
| Draw | Draw thin lines, thick lines, or polygons on the image. |
| Magnifier | |
| Measurement | |
| Share View | |
| Side by Side Viewer | |
| Heat Map | |
| Labeling | |
| Segment | |
| Bug Report | |
| Reviewed |
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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 your mouse to control the bounding box and drag it up, down, left, and right to see different parts of the main content window.
Using the Lymphocyte & Plasma Cell Annotation App
From caMicroscope you can launch the Lymphocyte & Plasma Cell Annotation App by clicking on the caMicroscope toolbar. This app allows you to view and modify annotations related to lymphocyte and plasma cells.
The following tools are available on the toolbar.
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Tool
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Name
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Purpose
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Home
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Return to the caMicroscope home page
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caMicroscope
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Return to the caMicroscope application
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Filter Markups
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View only those markups associated with selected algorithms. For more information, see page 8.
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Show/Hide Markups
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View the image with or without markups.
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Decrease Opacity
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Decrease the opacity of the selected markup(s), making it/them more transparent.
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Increase Opacity
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Increase the opacity of the selected markup(s), making it/them less transparent.
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Show Weight Panel
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This panel allows you to adjust the automatic lymphocyte prediction results for this slide, with the options described below.
- Lymphocyte Sensitivity bar:
Adjust the sensitivity of lymphocyte prediction.
Choose a higher volume for more predicted lymphocyte regions.
- Necrosis Specificity bar:
Adjust the specificity of necrosis prediction.
Choose a higher volume for more predicted lymphocyte regions.
- Lymphocyte Prediction box:
Show lymphocyte prediction without necrosis filtering.
- Necrosis Prediction box:
Show necrosis prediction.
- Lym Prediction with Nec Filtering box:
Show lymphocyte prediction with necrosis filtering (recommended).
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Free Line Markup
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Switch User
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If you are a super user, click this button to review and change other people’s annotations.
Using the Segment Curation App
Use the Segment Curation App to curate segmentation results.
The Segment Curation App has the following tools.
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Tool
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Name
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Purpose
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Home
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Return to the caMicroscope home page.
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Free Line Markup
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Draw thin lines, thick lines, or polygons on the image.
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Save ViewPort
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For a selected algorithm, save the ViewPort.
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Save Rectangle and Delete Annotations in This Area
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For an area based on a selected algorithm, save the rectangle and delete the annotations.
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Filter Markups
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Generate Composite Dataset
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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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- Log in to caMicroscope and then click the icon for FeatureScape.
The SlideSelect page appears. - 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.
- Click a link in the caMicroscope column to view the diagnostic image in caMicroscope.
- 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. - 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.
Viewing Scatterplots
To the right of the feature correlation plot is a scatterplot based on the computed feature values. The scatterplot shows how objects are distributed. Zoom in by selecting a region to look at the distribution in more detail.
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Selecting a Region on the Scatterplot
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