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    8 repositories

    • Xenium_NMF

      Public
      Non-negative factorization for xenium data in pyro
      Python
      •
      Apache License 2.0
      •0•0•2•0•Updated Aug 16, 2025Aug 16, 2025

    • cell2location

      Public
      Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)
      Python
      •
      Apache License 2.0
      •67•372•114•13•Updated Jun 23, 2025Jun 23, 2025

    • cell2fate

      Public
      Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.
      Python
      •
      Apache License 2.0
      •7•79•8•0•Updated Mar 20, 2025Mar 20, 2025

    • webatlas-pipeline

      Public
      A data pipeline built in Nextflow to process spatial and single-cell experiment data for visualisation in WebAtlas
      Python
      •
      MIT License
      •10•1•0•0•Updated Jun 26, 2023Jun 26, 2023

    • image-station

      Public
      Image visualization in a browser with batteries included (mirroring from internal gitlab)
      Dockerfile
      •0•2•0•0•Updated Apr 6, 2023Apr 6, 2023

    • feature_reg

      Public archive
      Feature based registration for fluorescence microscopy images
      Python
      •
      Apache License 2.0
      •3•4•1•0•Updated May 25, 2022May 25, 2022

    • opt_flow_reg

      Public archive
      Optical flow based registration for fluorescence microscopy images
      Python
      •
      Apache License 2.0
      •1•3•0•0•Updated May 16, 2022May 16, 2022

    • CountCorrect

      Public
      CountCorrect: Background removal for Nanostring WTA data
      Python
      •3•4•3•0•Updated Oct 19, 2021Oct 19, 2021