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!
This is a R toolkit and developer version package to estimate multidimensional aspects of greenness and nature exposure, such as availability, accessibility and visibility using various geospatial data and models
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.
Nextflow version of Sopa - spatial omics pipeline and analysis
Download and Convert METASPACE datasets to common formats such as AnnData or SpatialData
Geospatial Ontology to support the Documentation of Minor Historical Centres
Read-only Rust CLI for inspecting Zarr, OME-Zarr and SpatialData metadata locally, on S3 and over HTTP.
Live births in Scotland 2021 - Exercise on spatial vector data with R - RMarkdown file
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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