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BioImageTools

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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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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

Type Language Sort

ome-zarr-fiji-java Public
A drag-and-drop gateway of OME-Zarrs into Fiji.

BioImageTools/ome-zarr-fiji-java's past year of commit activity

Java 5 BSD-2-Clause 2 12 3 Updated Aug 25, 2026
capability-manifest Public

BioImageTools/capability-manifest's past year of commit activity

TypeScript 4 0 0 0 Updated Jun 16, 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
nf-module-aggregator Public
Nextflow Module Catalog

BioImageTools/nf-module-aggregator's past year of commit activity

Astro 2 0 0 0 Updated Mar 17, 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
ngff-transformations Public

BioImageTools/ngff-transformations's past year of commit activity

Jupyter Notebook 8 BSD-3-Clause 2 1 1 Updated Nov 16, 2025
vizarr Public Forked from hms-dbmi/vizarr
A minimal Zarr image viewer based on Viv.

BioImageTools/vizarr's past year of commit activity

TypeScript 0 MIT 41 0 0 Updated Nov 13, 2025
zarr-benchmarks Public Forked from HEFTIEProject/zarr-benchmarks

BioImageTools/zarr-benchmarks's past year of commit activity

Python 0 BSD-3-Clause 4 0 0 Updated Nov 13, 2025
zarr-chunk-benchmarking Public
2024 OME-Zarr Hackathon project for benchmarking read performance of chunk sizing on different storage environments

BioImageTools/zarr-chunk-benchmarking's past year of commit activity

Python 2 0 0 0 Updated Nov 12, 2025

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