We are working to build native support for ROI-based analysis on the Portal. However, this is feature is not yet available.

In the meantime, we recommend the following workarounds to perform ROI-based analysis:

1. Annotations from ROIs in Visualizer to Workbench: Create cell annotations that indicate whether each cell is within an ROI drawn within the Visualizer (see Creating Cell Annotations from Story/ROIs). Then, through our ‣ add-on, you can pull and operate on these and any other cell annotations generated on the Portal. You can easily subset your cells to those within the drawn ROI(s), then perform additional analysis or data visualization, and push any resulting cell annotations back to the Portal.
   • This workflow allows for the creation of Explorer versions containing cells only within the ROI(s), when paired with a custom QC annotation that excludes all cells in the Region(s) that do not fall within the ROI(s). However, because new Region(s) are not created on Portal, the only analysis tools that will be available on Portal for the subsetted cells are the Visualizer and Explorer. All other analysis steps (i.e., QC, cell phenotyping, neighborhood analysis, neighborhood analysis) must be performed on the subsetted cells on Workbench.
2. Image Splitter Workflow in Portal: To work with a smaller area within a single Region, you can perform an image split using the Image Splitter Panel. This will create new Regions containing a sub-area of your original Region(s), allowing you to perform segmentation and downstream analysis on only the area(s) of interest.
   • Existing segmentation and cell annotations for the original (whole) Region(s) will not be associated with the newly split Region(s). We recommend performing image splitting prior to completing cell phenotyping to avoid duplicating work. If you require using existing annotations, please see option 1.
   • Note that proceeding with analysis on the combined set of newly split and the original Region(s) could limit proper interpretation of cohort comparisons in the Explorer. We recommend only proceeding with one or the other, or analyzing them separately to avoid this issue.

Below is a table summarizing pros and cons of each of these two options:

• Use existing regions and cell annotations
• Push new annotations back to Portal | - Requires Workbench add-on
• As new regions are not created on Portal, the cells within ROIs can only be analyzed using the Visualizer and Explorer | | Image Splitter Workflow | - Visually split out (sub)regions for analysis
• Use any apps/extensions in the Analysis Toolkit | - Cell segmentation and annotation must be re-run, as new (sub)regions will be created
• Combined analysis of original and new (sub)regions is not recommended |