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spatialdataHere are 18 public repositories matching this topic...Language: All
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Accessible and interoperable whole slide image analysis for digital pathology in Python
python bioinformatics deep-learning medical-imaging cell-segmentation digital-pathology pathology whole-slide-imaging computational-pathology histopathology spatialdata foundation-models scverse
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)
python tiles tiff gis tiling raster remote-sensing satellite-imagery map-tiles spatialdata geotiler tiling-image geotile gistile tiff-tile
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
Convert mass spectrometry imaging data (Bruker, Waters, PHI, imzML), with ion mobility and MS/MS, into the open SpatialData/Zarr format
bioinformatics scientific-computing mass-spectrometry msi bruker data-conversion maldi msms ion-mobility imzml omics-data-integration mass-spectrometry-imaging timstof zarr spatialdata pasef spatial-omics scverse m4i-cuypers-group ecuypers-group
Interoperability between SpatialData and the Xenium Explorer
Nextflow version of Sopa - spatial omics pipeline and analysis
workflow pipeline nextflow segmentation spatial-proteomics nf-core spatial-transcriptomics spatialdata spatial-omics
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%).
bioinformatics reproducible-research single-cell sensitivity-analysis spatial-transcriptomics scanpy spatialdata squidpy pipeline-robustness
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
SoPA companion: stain segmentation and live proseg for SpatialData from a notebook, with a mixing check and Compare. A companion to sopa.
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