Q&A

Basic

What is SpatialTis?

SpatialTis is a spatial analysis toolkit for single-cell multiplexed tissue data.

How parallel processing works?

Following functions in spatialtis can have parallel processing supported by Ray, use argument mp=True to enable.

• spatialtis.read_ROIs

• spatialtis.spatial_distribution()

• spatialtis.spatial_heterogeneity()

• spatialtis.hotspot()

• spatialtis.exp_neighcells()

• spatialtis.exp_neighexp()

These are implemented in rust, it will automatically run in parallel, supported by rayon.

• spatialtis.Neighbors.find_neighbors()

• spatialtis.spatial.neighborhood_analysis()

• spatialtis.spatial.spatial_enrichment_analysis()

MacOS Issues

Do you want the application “Python.app” to accept the incoming network connection?

If there are lots of these windows pop up on Mac, it’s cause by Ray. If you find it annoying, the simplest solution is to turn off your firework (with safety risk) or add it into the firewall white list. Another solution from this stackoverflow answer might also be helpful.