What cell-neighborhood analysis tools are available for Pyxa data?

Pyxa Studio is our visualization software and does not perform neighborhood analysis itself. However, Pyxa data can be analyzed with the same tools used in other spatial biology workflows.

The XYZ coordinates in Cell_metadata.csv can be used to build spatial neighbor graphs. These support analysis of recurring cell-type neighborhood composition, proximity-based cell co-localization and ligand–receptor interaction patterns. Tools that support this include Squidpy (Python), Giotto (R), Monkeybread (Python) and stLearn (Python).