Skip to content

@BioImageTools BioImageTools

Change the repository type filter

All

    Repositories list

    18 repositories

    • ome-zarr-fiji-java

      Public
      A drag-and-drop gateway of OME-Zarrs into Fiji.
      Java
      •
      BSD 2-Clause "Simplified" License
      •1•2•12•6•Updated Mar 26, 2026Mar 26, 2026

    • nf-module-aggregator

      Public
      Nextflow Module Catalog
      Astro
      •0•1•0•0•Updated Mar 17, 2026Mar 17, 2026

    • capability-manifest

      Public
      TypeScript
      •0•3•0•0•Updated Feb 12, 2026Feb 12, 2026

    • nextflow-modules

      Public
      nf-core-compatible modules for Nextflow
      Nextflow
      •
      BSD 3-Clause "New" or "Revised" License
      •2•4•9•0•Updated Jan 28, 2026Jan 28, 2026

    • biomero-schema

      Public
      A spec for BIOMERO workflows developed at the GLOBIAS 2025 Hackathon
      Python
      •0•1•2•1•Updated Nov 19, 2025Nov 19, 2025

    • ngff-transformations

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •2•8•1•0•Updated Nov 16, 2025Nov 16, 2025

    • vizarr

      Public
      A minimal Zarr image viewer based on Viv.
      TypeScript
      •
      MIT License
      •39•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•4•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•3•3•0•Updated Nov 10, 2023Nov 10, 2023
    ProTip! Don't forget that you can create saved views to keep track of your most important repositories!