Repositories list

• spec-bioimage-io

  Public
  Specification for the bioimage.io model description file.

  Python

  •

  MIT License

  •16•21•43•7•Updated Sep 18, 2025Sep 18, 2025

• core-bioimage-io-python

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

  deep-learningbioimagingbioimage-analysis+ 1bioimage-infomatics

  Jupyter Notebook

  •

  MIT License

  •22•33•64•7•Updated Sep 18, 2025Sep 18, 2025

• bioimageio-colab

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

  Python

  •

  MIT License

  •0•5•4•0•Updated Sep 15, 2025Sep 15, 2025

• collection

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

  Python

  •9•2•10•3•Updated Sep 8, 2025Sep 8, 2025

• hypha

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

  Python

  •

  MIT License

  •8•0•0•1•Updated Sep 3, 2025Sep 3, 2025

• bioimage.io

  Public
  TypeScript

  •0•3•2•0•Updated Aug 22, 2025Aug 22, 2025

• use-cases

  Public
  Drafting the use-cases for the publication

  Python

  •

  MIT License

  •3•2•2•3•Updated Jul 30, 2025Jul 30, 2025

• JDLL

  Public
  The Java library to run Deep Learning models

  javaimglib2pytorch+ 4onnxbioimage-iodeep-learningtensorflow

  Java

  •

  Apache License 2.0

  •6•32•14•2•Updated Jul 22, 2025Jul 22, 2025

• onnx-java-interface

  Public
  Java

  •

  Apache License 2.0

  •0•1•0•0•Updated Jul 22, 2025Jul 22, 2025

• pytorch-java-interface-javacpp

  Public
  Java

  •

  Apache License 2.0

  •0•0•0•0•Updated Jul 22, 2025Jul 22, 2025

• pytorch-java-interface

  Public
  Java

  •

  Apache License 2.0

  •0•1•0•0•Updated Jul 22, 2025Jul 22, 2025

• tensorflow-2-java-interface-0.5.0

  Public
  Java

  •

  Apache License 2.0

  •0•0•0•0•Updated Jul 22, 2025Jul 22, 2025

• tensorflow-2-java-interface-0.2.0

  Public
  Java

  •

  Apache License 2.0

  •0•1•0•0•Updated Jul 22, 2025Jul 22, 2025

• tensorflow-2-java-interface

  Public
  Java

  •

  Apache License 2.0

  •1•2•0•0•Updated Jul 22, 2025Jul 22, 2025

• tensorflow-1-java-interface

  Public
  Java

  •

  Apache License 2.0

  •0•2•0•0•Updated Jul 22, 2025Jul 22, 2025

• dev.bioimage.io

  Public
  0•0•0•0•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

  •22•60•76•28•Updated Jun 30, 2025Jun 30, 2025

• bioimageio.spec-feedstock

  Public
  A conda-smithy repository for bioimageio.spec.

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

  •3•0•0•0•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

  •0•1•0•0•Updated May 27, 2025May 27, 2025

• dev.collection

  Public
  Development fork of bioimage-io/collection

  Python

  •9•0•0•0•Updated Apr 25, 2025Apr 25, 2025

• bioimageio-chatbot

  Public
  Your Personal Assistant in Computational Bioimaging.

  Jupyter Notebook

  •

  MIT License

  •12•44•5•1•Updated Mar 28, 2025Mar 28, 2025

• bioengine

  Public
  Jupyter Notebook

  •

  MIT License

  •0•10•3•1•Updated Feb 10, 2025Feb 10, 2025

• bioimageio-uploader

  Public
  Svelte

  •2•1•22•0•Updated Nov 17, 2024Nov 17, 2024

• collection-bioimage-io

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

  Python

  •9•5•68•19•Updated Jul 8, 2024Jul 8, 2024

• hypha-helm-charts

  Public
  Smarty

  •

  MIT License

  •2•0•0•0•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

  •2•4•1•0•Updated Jun 19, 2024Jun 19, 2024

• bioimageio-uploader-service

  Public
  Review service for bioimage.io uploader

  Python

  •0•0•5•0•Updated Jun 18, 2024Jun 18, 2024

• bioengine-k8s

  Public
  Python

  •

  MIT License

  •1•0•0•0•Updated Jun 18, 2024Jun 18, 2024

• bioengine-model-runner

  Public
  Python

  •2•3•5•1•Updated Jun 12, 2024Jun 12, 2024

• bioimage-io.github.io

  Public
  HTML

  •0•0•0•0•Updated Jun 6, 2024Jun 6, 2024