spatialtis.cell_density

spatialtis.cell_density(data, ratio=1.0, export_key='cell_density', **kwargs)

Calculating cell density in each ROI.

The size of each ROI will be auto-computed as convex hull of all the cells in a ROI.

Parameters

dataAnnData

The AnnData to work with.

ratiofloat, default: 1.0

The ratio between the unit used in your dataset and real length unit. ratio = Dataset unit / real length unit. For example, if the resolution of your dataset is 1μm, but you want to use 1mm as unit, then you should set the ratio as 0.001, 1 pixel = 0.001mm.

export_keystr

The key used to store result.

**kwargs

Config for the analysis, for details check spatialtis.abc.AnalysisBase.