How to Compare two ROIs?¶

This guide explains how to compare two Regions of Interest (ROIs) to perform differential analysis.

1. Create two ROIs¶

For each ROI, follow the steps in How to Create a ROI to create it.

2. Compare two ROIs¶

The following example is comparing the granule cell layer of dentate gyrus (pale yellow) with pyramidal layer of Ammon's horn (berry) in the hippocampus.

ROI Compare

1). Navigate to Compare Page: Click the Compare button in the ROI Operations section.
2). Select ROIs: Use the dropdown menus to select the two ROIs you wish to compare.

ROI Selection

Please aware that the two ROIs for comparison should not have any overlap.

CartoScope automatically checks for overlap and will alert you if the selected ROIs have any overlap.

3. View the details of the ROI comparison¶

You can inspect the comparison results in three modes: by genes, by factor set, or by a specific factor.

Interaction with Comparison results

For each of the three ways, you can:

Export: Download the comparison results to a file.
Inspect: Filter, sort, and search the results table.
Add Genes to Map: Click the + button next to a gene name to visualize it on the map.