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@BioImageTools

BioImageTools

README.md

BioImageTools

Shared GitHub organization for work related to OME-Zarr and scalable bioimage analysis workflows.

This org was created at the 2023 Next generation bioimage analysis workflows hackathon held at the BioVisionCenter at UZH, for the purposes of continuing collaboration and innovation on NGFF-based and FAIR image processing workflows. Continued at the 2024 OME-NGFF workflows hackathon and the 2025 OME-NGFF workflows hackathon

We are interested in...

  • Bioimage tools which consume and/or produce OME-Zarr
  • OCI containers
  • Nextflow modules and subworkflows
  • Galaxy integrations
  • Fractal integrations
  • OME-Zarr usage examples
  • OME-Zarr performance evaluation
  • OME-Zarr 0.5 tool evaluation
  • ...

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  1. ome-zarr-image-analysis-nextflow ome-zarr-image-analysis-nextflow Public

    Basic example of using OME-Zarr in a Nextflow pipeline

    Jupyter Notebook 21 4

Repositories

Showing 10 of 23 repositories
  • bioimage-task-vocabulary Public
    BioImageTools/bioimage-task-vocabulary's past year of commit activity
    1 MIT 0 0 1 Updated Nov 9, 2026
  • capability-manifest Public
    BioImageTools/capability-manifest's past year of commit activity
    TypeScript 4 0 0 0 Updated Nov 6, 2026
  • ome-zarr-skills Public

    Agentic Skills for OME-Zarr

    BioImageTools/ome-zarr-skills's past year of commit activity
    Python 4 BSD-3-Clause 2 0 1 Updated Nov 6, 2026
  • zarr-convention-provenance Public

    Workflow provenance convention for Zarr: the software, inputs and checks behind a node

    BioImageTools/zarr-convention-provenance's past year of commit activity
    Groovy 1 Apache-2.0 1 0 0 Updated Nov 6, 2026
  • fractal-multistep-nextflow Public
    BioImageTools/fractal-multistep-nextflow's past year of commit activity
    Nextflow 0 BSD-3-Clause 0 0 0 Updated Nov 6, 2026
  • 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.

    BioImageTools/ome-zarr-fiji-java's past year of commit activity
    Java 10 BSD-2-Clause 7 23 4 Updated Nov 6, 2026
  • nf-module-aggregator Public

    Nextflow Module Catalog

    BioImageTools/nf-module-aggregator's past year of commit activity
    Astro 2 0 0 0 Updated Nov 5, 2026
  • biomero-schema Public

    A spec for BIOMERO workflows developed at the GLOBIAS 2025 Hackathon

    BioImageTools/biomero-schema's past year of commit activity
    Python 1 Apache-2.0 1 2 0 Updated Jun 3, 2026
  • scijava-context-test Public

    The only purpose of this repo is to test a potential memory leak in scijava context

    BioImageTools/scijava-context-test's past year of commit activity
    Java 0 BSD-3-Clause 0 0 0 Updated Apr 14, 2026
  • nextflow-modules Public

    nf-core-compatible modules for Nextflow

    BioImageTools/nextflow-modules's past year of commit activity
    Nextflow 4 BSD-3-Clause 2 13 0 Updated Jan 28, 2026
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