Accessible and interoperable whole slide image analysis for digital pathology in Python
Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoCycler / MACSima / etc.)
GeoTile is the python library for tiling the geographic raster data (eg. Tiff etc)
Single-cell spatial omics analysis that makes you happy!
Interoperability between SpatialData and the Xenium Explorer
A modern Python library for converting Mass Spectrometry Imaging (MSI) data into standardized SpatialData/Zarr format, enabling seamless integration with spatial omics analysis workflows.
Download and Convert METASPACE datasets to common formats such as AnnData or SpatialData
How much of a spatial transcriptomics result is the pipeline? One preprocessing choice at a time on Visium mouse brain gives median ARI 0.83, and with clusters matched between runs the neighbourhood-enrichment conclusion keeps 19-84% of its pairs (median 53%).
GPU-accelerated Python pipeline for image-based spatial omics, built on Sopa and SpatialData
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