Repositories list

• collection

  Public
  Maintains the resources displayed on bioimage.io (Successor to collection-bioimage-io)

  Python

  •1111 forks•22 stars•1010 issues•11 pull request•Updated Apr 12, 2026Apr 12, 2026

• bioimage.io

  Public
  Website for the BioImage Model zoo -- a model zoo for bioimage analysis.

  TypeScript

  •44 forks•99 stars•99 issues•33 pull requests•Updated Apr 11, 2026Apr 11, 2026

• spec-bioimage-io

  Public
  Specification for the bioimage.io model description file.

  Jupyter Notebook

  •

  MIT License

  •1515 forks•2323 stars•2929 issues•77 pull requests•Updated Apr 9, 2026Apr 9, 2026

• JDLL

  Public
  The Java library to run Deep Learning models

  javadeep-learningimglib2+ 4

  javadeep-learningimglib2tensorflowpytorchonnxbioimage-io

  Java

  •

  Apache License 2.0

  •66 forks•3434 stars•1414 issues•00 pull requests•Updated Apr 8, 2026Apr 8, 2026

• core-bioimage-io-python

  Public
  Python libraries for loading, running and packaging bioimage.io models

  deep-learningbioimagingbioimage-analysis+ 1

  deep-learningbioimagingbioimage-analysisbioimage-infomatics

  Jupyter Notebook

  •

  MIT License

  •2121 forks•3535 stars•5959 issues•77 pull requests•Updated Apr 8, 2026Apr 8, 2026

• bioimageio-colab

  Public
  Collaborative image annotation and model training with human in the loop

  Python

  •

  MIT License

  •00 forks•66 stars•33 issues•00 pull requests•Updated Nov 28, 2025Nov 28, 2025

• hypha

  Public
  A serverless application framework for large-scale data management and AI model serving

  Python

  •

  MIT License

  •1414 forks•00 stars•00 issues•11 pull request•Updated Sep 3, 2025Sep 3, 2025

• use-cases

  Public
  Drafting the use-cases for the publication

  Python

  •

  MIT License

  •33 forks•22 stars•22 issues•44 pull requests•Updated Jul 30, 2025Jul 30, 2025

• onnx-java-interface

  Public
  Java

  •

  Apache License 2.0

  •00 forks•11 star•00 issues•00 pull requests•Updated Jul 22, 2025Jul 22, 2025

• pytorch-java-interface-javacpp

  Public
  Java

  •

  Apache License 2.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 22, 2025Jul 22, 2025

• pytorch-java-interface

  Public
  Java

  •

  Apache License 2.0

  •00 forks•11 star•00 issues•00 pull requests•Updated Jul 22, 2025Jul 22, 2025

• tensorflow-2-java-interface-0.5.0

  Public
  Java

  •

  Apache License 2.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 22, 2025Jul 22, 2025

• tensorflow-2-java-interface-0.2.0

  Public
  Java

  •

  Apache License 2.0

  •00 forks•11 star•00 issues•00 pull requests•Updated Jul 22, 2025Jul 22, 2025

• tensorflow-2-java-interface

  Public
  Java

  •

  Apache License 2.0

  •11 fork•22 stars•00 issues•00 pull requests•Updated Jul 22, 2025Jul 22, 2025

• tensorflow-1-java-interface

  Public
  Java

  •

  Apache License 2.0

  •00 forks•22 stars•00 issues•00 pull requests•Updated Jul 22, 2025Jul 22, 2025

• dev.bioimage.io

  Public
  00 forks•00 stars•00 issues•00 pull requests•Updated Jul 1, 2025Jul 1, 2025

• archive.bioimage.io

  Public
  Website for the BioImage Model zoo -- a model zoo for bioimage analysis.

  CSS

  •

  MIT License

  •2222 forks•6060 stars•7575 issues•2828 pull requests•Updated Jun 30, 2025Jun 30, 2025

• bioimageio.spec-feedstock

  Public
  A conda-smithy repository for bioimageio.spec.

  BSD 3-Clause "New" or "Revised" License

  •33 forks•00 stars•00 issues•00 pull requests•Updated Jun 27, 2025Jun 27, 2025

• AI4Life_CommunityEvent_W1S2

  Public
  Session 1: Creating, Uploading, Deploying and Containerizing BioImage Model Zoo Models

  Jupyter Notebook

  •

  BSD 2-Clause "Simplified" License

  •00 forks•11 star•00 issues•00 pull requests•Updated May 27, 2025May 27, 2025

• dev.collection

  Public
  Development fork of bioimage-io/collection

  Python

  •1111 forks•00 stars•00 issues•00 pull requests•Updated Apr 25, 2025Apr 25, 2025

• bioimageio-chatbot

  Public
  Your Personal Assistant in Computational Bioimaging.

  Jupyter Notebook

  •

  MIT License

  •1313 forks•4545 stars•55 issues•11 pull request•Updated Mar 28, 2025Mar 28, 2025

• bioengine

  Public
  Jupyter Notebook

  •

  MIT License

  •11 fork•1313 stars•33 issues•11 pull request•Updated Feb 10, 2025Feb 10, 2025

• bioimageio-uploader

  Public
  Svelte

  •22 forks•11 star•2222 issues•00 pull requests•Updated Nov 17, 2024Nov 17, 2024

• collection-bioimage-io

  Public
  (deprecated in favor of bioimage-io/collection) RDF collection for BioImage.IO

  Python

  •1010 forks•55 stars•6868 issues•1919 pull requests•Updated Jul 8, 2024Jul 8, 2024

• hypha-helm-charts

  Public
  Smarty

  •

  MIT License

  •22 forks•00 stars•00 issues•00 pull requests•Updated Jun 19, 2024Jun 19, 2024

• Workshop-June2024-Madrid

  Public
  Repository for hosting all resources and details related to the AI4Life and BioImage Model Zoo workshop scheduled for June 2024 in Madrid.o

  Jupyter Notebook

  •

  MIT License

  •22 forks•44 stars•11 issue•00 pull requests•Updated Jun 19, 2024Jun 19, 2024

• bioimageio-uploader-service

  Public
  Review service for bioimage.io uploader

  Python

  •00 forks•00 stars•55 issues•00 pull requests•Updated Jun 18, 2024Jun 18, 2024

• bioengine-k8s

  Public
  Python

  •

  MIT License

  •11 fork•00 stars•00 issues•00 pull requests•Updated Jun 18, 2024Jun 18, 2024

• bioengine-model-runner

  Public
  Python

  •22 forks•33 stars•55 issues•11 pull request•Updated Jun 12, 2024Jun 12, 2024

• bioimage-io.github.io

  Public
  HTML

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jun 6, 2024Jun 6, 2024