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    19 repositories

    • ome-zarr-fiji-java

      Public
      Fiji/ImageJ plugin that brings OME-Zarr into everyday Fiji use: drag & drop, clipboard, menu and scripting, in ImageJ or BigDataViewer.
      imagejimglib2fiji
      imagejimglib2fijibigdataviewerzarrome-zarr
      Java
      •
      BSD 2-Clause "Simplified" License
      •6•8•20•4•Updated Oct 26, 2026Oct 26, 2026

    • capability-manifest

      Public
      TypeScript
      •0•4•0•0•Updated Sep 14, 2026Sep 14, 2026

    • biomero-schema

      Public
      A spec for BIOMERO workflows developed at the GLOBIAS 2025 Hackathon
      Python
      •
      Apache License 2.0
      •1•1•2•0•Updated Jun 3, 2026Jun 3, 2026

    • scijava-context-test

      Public
      The only purpose of this repo is to test a potential memory leak in scijava context
      Java
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Apr 14, 2026Apr 14, 2026

    • nf-module-aggregator

      Public
      Nextflow Module Catalog
      Astro
      •0•2•0•0•Updated Mar 17, 2026Mar 17, 2026

    • nextflow-modules

      Public
      nf-core-compatible modules for Nextflow
      Nextflow
      •
      BSD 3-Clause "New" or "Revised" License
      •2•4•13•0•Updated Jan 28, 2026Jan 28, 2026

    • ngff-transformations

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •2•8•1•1•Updated Nov 16, 2025Nov 16, 2025

    • vizarr

      Public
      A minimal Zarr image viewer based on Viv.
      TypeScript
      •
      MIT License
      •43•0•0•0•Updated Nov 13, 2025Nov 13, 2025

    • zarr-benchmarks

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •4•0•0•0•Updated Nov 13, 2025Nov 13, 2025

    • 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 12, 2025Nov 12, 2025

    • .github

      Public
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Nov 5, 2025Nov 5, 2025

    • iss-nf

      Public
      Reusable in-situ sequencing analysis workflow orchestrated by Nextflow
      pythonscalableomics
      pythonscalableomicsspatial-transcriptomicsnextflow-pipelinereusable-workflows
      Python
      •
      MIT License
      •1•6•2•0•Updated Oct 21, 2025Oct 21, 2025

    • ome-zarr-image-analysis-nextflow

      Public
      Basic example of using OME-Zarr in a Nextflow pipeline
      Jupyter Notebook
      •
      MIT License
      •4•21•6•0•Updated Jul 15, 2025Jul 15, 2025

    • 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

    • 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

    • 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•4•3•0•Updated Nov 10, 2023Nov 10, 2023
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