Regions of Interest

Regions of Interest (ROIs) that have been drawn as notes under a story are useful pieces of data that can provide new visualizations and insights.

These ROIs are saved as notes and can be combined with any segmentation version for that study to annotate all cells which reside within those ROIs.

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Creating Story Annotations

  1. From the Stories section of the visualizer (right hand side) click into any of the stories that you have created.

    Screen Shot 2022-08-12 at 12.13.29 PM.png

  2. Click on Generate Cell Annotations:

  3. This will prompt you to select a segmentation version:

    Screen Shot 2022-10-11 at 9.50.46 PM.png

  4. Choose the segmentation version that you would like to use and click Create Annotations.

  5. This will kick off our internal pipelines to label all of the cells within the ROIs defined by notes in that story.

    1. Each note will be represented by its own annotation set, which will be named by the title of that note (e.g. a note titled “Tumor boundary” will create an annotation set with the name “Tumor boundary”).
    2. Cells within the ROIs defined by each note will be annotated with the title of that note (e.g. a note titled “Tumor boundary” will label all cells within the ROIs defined in that note “Tumor boundary”). Cells outside those ROIs will be labeled “other”.

  6. We will notify you when the annotation pipeline has completed! You will then be able to use the annotation set for downstream analysis on workbench.

  7. If you would like to visualize the new annotation set to verify that the ROIs included the correct cells, you can generate an overlay in the visualizer.

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