Spatial Omics Python Packages

napari-spatialdata

Interactive visualization of spatial omics data

sopa

Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoCycler / MACSima / etc.)

thyra

A modern Python library for converting Mass Spectrometry Imaging (MSI) data into standardized SpatialData/Zarr format, enabling seamless integration with spatial omics analysis workflows.

novae

Graph-based foundation model for spatial transcriptomics data. Zero-shot spatial domain inference, batch-effect correction, and many other features.

harpy-analysis

Single-cell spatial omics analysis that makes you happy!

omero-vitessce

OMERO.web plugin for the Vitessce multimodal data viewer.

senoquant-stardist-ext

Quantifying senescence, the easy way.

pybanksy

BANKSY: Spatial Clustering Algorithm that Unifies Cell-Typing and Tissue Domain Segmentation. Python package for spatial transcriptomics analysis.

nichecompass

End-to-end analysis of spatial multi-omics data

cell-gps

Cell-GPS spatial topology analysis for spatial omics data.

senoquant

napari plugin for spatial quantification of senescence markers in tissue imaging

cell-decipher

DECIPHER for learning high-fidelity disentangled embeddings from spatial omics data

spatialtis

Ultra-fast spatial analysis toolkit for large-scale spatial single-cell data

spatialdata-xenium-explorer

Converting any SpatialData object into files that can be open by the Xenium Explorer

expression-copilot

Quantifying predictability of gene expression from histology image