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
A modern Python library for converting Mass Spectrometry Imaging (MSI) data into standardized SpatialData/Zarr format, enabling seamless integration with spatial omics analysis workflows.
Interoperability between SpatialData and the Xenium Explorer
Nextflow version of Sopa - spatial omics pipeline and analysis
Download and Convert METASPACE datasets to common formats such as AnnData or SpatialData
Quality metrics for imaging-based spatial proteomics: segmentation, signal-to-background, normalization, marker distribution and technical-covariate diagnostics.
Specification for the SpatialData format
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
To associate your repository with the spatialdata topic, visit your repo's landing page and select "manage topics."