Spatialdata 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.)

lazyslide

Accessible and interoperable whole slide image analysis for digital pathology in Python

harpy-analysis

Single-cell spatial omics analysis that makes you happy!

geotile

GeoTile is the python library for tiling the geographic raster data (eg. Tiff etc)

metaspace-converter

Download and Convert METASPACE datasets to common formats such as AnnData or SpatialData

spatialdata-xenium-explorer

Interoperability between SpatialData and the Xenium Explorer