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 SpatialData/Zarr format - your portal to spatial omics

novae

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

nichecompass

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

harpy-analysis

Single-cell spatial omics analysis that makes you happy!

omero-vitessce

OMERO Vitessce multimodal data viewer plugin for OMERO.web

senoquant-stardist-ext

Quantifying senescence, the easy way.

senoquant

napari plugin for spatial quantification of senescence markers in tissue imaging

pybanksy

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

cell-decipher

DECIPHER for learning disentangled cellular embeddings in large-scale heterogeneous spatial omics data

spatialtis

Spatial analysis toolkit for single cell multiplexed tissue data

spatialdata-xenium-explorer

Interoperability between SpatialData and the Xenium Explorer

expression-copilot

Quantifying predictability of gene expression from histology image