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    13 repositories

    • iss-nf

      Public
      Reusable in-situ sequencing analysis workflow orchestrated by Nextflow
      pythonscalableomicsspatial-transcriptomicsnextflow-pipelinereusable-workflows
      Python
      •
      MIT License
      •0•2•2•0•Updated May 15, 2025May 15, 2025

    • .github

      Public
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Mar 13, 2025Mar 13, 2025

    • ome-zarr-fiji-java

      Public
      A drag-and-drop gateway of OME-Zarrs into Fiji.
      Java
      •
      BSD 2-Clause "Simplified" License
      •0•0•0•0•Updated Jan 16, 2025Jan 16, 2025

    • ngff-transformations

      Public
      Python
      •
      MIT License
      •0•4•1•0•Updated Nov 23, 2024Nov 23, 2024

    • zarr-chunk-benchmarking

      Public
      2024 OME-Zarr Hackathon project for benchmarking read performance of chunk sizing on different storage environments
      Python
      •0•2•0•0•Updated Nov 22, 2024Nov 22, 2024

    • single-file-ome-ngff

      Public
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Nov 21, 2024Nov 21, 2024

    • ome-zarr-parallel-write

      Public
      ome-zarr-parallel-write outcome @ OME-NGFF workflow hackathon
      0•0•0•0•Updated Nov 19, 2024Nov 19, 2024

    • ome-zarr-image-analysis-nextflow

      Public
      Basic example of using OME-Zarr in a Nextflow pipeline
      Jupyter Notebook
      •
      MIT License
      •2•16•7•0•Updated Nov 16, 2024Nov 16, 2024

    • containers

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•3•1•0•Updated Sep 26, 2024Sep 26, 2024

    • test-datasets

      Public
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•Updated Apr 2, 2024Apr 2, 2024

    • nextflow-modules

      Public
      nf-core-compatible modules for Nextflow
      Nextflow
      •
      BSD 3-Clause "New" or "Revised" License
      •1•2•2•0•Updated Jan 17, 2024Jan 17, 2024

    • baysor-nextflow-module

      Public
      Nextflow module to use Baysor for cell segmentation in imaging-based Spatial Transcriptomics
      Python
      •
      MIT License
      •0•2•0•0•Updated Dec 1, 2023Dec 1, 2023

    • ome-zarr-examples

      Public
      Collection of ome-zarr structures, for testing different NGFF validators
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•2•0•Updated Nov 10, 2023Nov 10, 2023