Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoCycler / MACSima / etc.)
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Sep 1, 2026 - Python
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spatialdata
Here are 14 public repositories matching this topic...
GeoTile is the python library for tiling the geographic raster data (eg. Tiff etc)
python tiles tiff gis tiling raster remote-sensing satellite-imagery map-tiles spatialdata geotiler tiling-image geotile gistile tiff-tile
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Sep 9, 2024 - Python
Single-cell spatial omics analysis that makes you happy!
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Sep 1, 2026 - Python
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
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Oct 12, 2025 - R
Interoperability between SpatialData and the Xenium Explorer
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Jul 31, 2024 - Python
A modern Python library for converting Mass Spectrometry Imaging (MSI) data into standardized SpatialData/Zarr format, enabling seamless integration with spatial omics analysis workflows.
bioinformatics scientific-computing mass-spectrometry msi bruker data-conversion imzml omics-data-integration mass-spectrometry-imaging zarr spatialdata spatial-omics m4i-cuypers-group ecuypers-group
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Sep 1, 2026 - Python
Nextflow version of Sopa - spatial omics pipeline and analysis
workflow pipeline nextflow segmentation spatial-proteomics nf-core spatial-transcriptomics spatialdata spatial-omics
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Sep 1, 2026 - Nextflow
Download and Convert METASPACE datasets to common formats such as AnnData or SpatialData
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Feb 27, 2026 - Python
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Jun 5, 2026 - Jupyter Notebook
RPuGB (Raeumliche Perturbations- und Gewebesimulations-Bibliothek) is a scientific Python library for spatial perturbation analysis, causal bystander decoupling, and in silico tissue simulation in functional genomics.
bioinformatics computational-biology causal-inference functional-genomics spatial-transcriptomics anndata spatialdata counterfactual-inference double-machine-learning synthetic-lethality regulatory-compliance diffusion-transformer eu-ai-act tissue-simulation reaction-diffusion-pde rocm-gpu crispr-knockout bystander-effects eurohpc-lumi 3rs-animal-replacement
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Aug 30, 2026 - Python
Geospatial Ontology to support the Documentation of Minor Historical Centres
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May 5, 2022
Read-only Rust CLI for inspecting Zarr, OME-Zarr and SpatialData metadata locally, on S3 and over HTTP.
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Aug 31, 2026 - Rust
Live births in Scotland 2021 - Exercise on spatial vector data with R - RMarkdown file
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Aug 31, 2024 - HTML
GPU-accelerated Python pipeline for image-based spatial omics, built on Sopa and SpatialData
python image-segmentation microscopy bioimage-analysis sopa qupath spatialdata spatial-omics stardist spatial-biology
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Aug 25, 2026 - Python
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