TissueMask: Spatial Boundary Mask Fitting for Point Coordinate Data

TissueMask provides fit_spatial_mask(), which fits polygon spatial masks to XY point coordinate data such as cell centroids or transcript locations from spatial transcriptomics and spatial proteomics experiments.

Four masking methods are available, supporting geometries of increasing topological complexity — from simple convex hulls to multi-polygon masks with internal voids and disconnected islands:

Method	Holes/Islands	Speed	Recommended for
"convex"	No	Instant	Sanity checks
"concave"	No	Fast	Simple non-convex shapes
"kde"	Yes	Moderate	Dense, smooth datasets
"raster"	Yes	Fast	Most use cases (default)

Part of TissueSuite

TissueMask is the first component of the TissueSuite package family developed at the Raredon Laboratory, Yale School of Medicine. The companion package TissueField uses TissueMask output to estimate steady-state molecular concentration fields via a diffusion–clearance PDE.

See also

fit_spatial_mask()

Author

Maintainer: Raredon Laboratory raredonlab@yale.edu