Spatial Omics Python Packages

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.

sopa

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

spatioloji-s

Python toolkit for image-based spatial transcriptomics (CosMx, MERFISH, Xenium). Unified data object for expression, polygons, and FOV images, plus QC, clustering, point- and polygon-based spatial statistics, and polygon-native cell-cell communication using real membrane contact geometry.

napari-spatialdata

Interactive visualization of spatial omics data

novae

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

milume

Milume: a thinking surface for spatial omics. Layer images, cells, and transcripts in one reactive notebook widget.

spatial-rx

Milume: a thinking surface for spatial omics. Layer images, cells, and transcripts in one reactive notebook widget.

harpy-analysis

Single-cell spatial omics analysis that makes you happy!

pybanksy

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

senoquant-stardist-ext

Quantifying senescence, the easy way.

omero-vitessce

OMERO.web plugin for the Vitessce multimodal data viewer.

senoquant

Quantifying senescence, the easy way.

nichecompass

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

cell-decipher

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

cell-gps

Cell-GPS spatial topology analysis for 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

spoqc

A modular framework for multimodal quality control (QC) of imaging-based spatially resolved transcriptomics (SRT).

histopia

Histology Spatial Topology for Omics Profiling and Inter-section Alignment