scimappro

scimappro is a Python toolkit for spatial single-cell analysis workflows. It provides preprocessing, analysis, and plotting utilities for AnnData objects and large .h5ad datasets.

Installation

pip install scimappro

Modules

• scimappro.pp: preprocessing helpers including mcmicro_to_scimap, rescale, combat, and log1p.
• scimappro.tl: analysis tools including neighborhood counts, neighborhood expression, phenotype assignment, clustering, UMAP, spatial distance, co-occurrence, proximity scores, fold change, and spatial similarity lookup.
• scimappro.pl: plotting helpers including bar plots and heatmaps.

Example

import scimappro as sp

# Preprocessing
# sp.pp.rescale(...)

# Analysis
# sp.tl.spatialDistance(...)

# Plotting
# sp.pl.heatmap(...)

License

See the project repository for license information.