Repositories list

• fidfab

  Public
  The enlightened computational science factory for expert research software engineers.

  Shell

  •

  MIT License

  •00 forks in fideus-labs/fidfab•11 star in fideus-labs/fidfab•00 issues in fideus-labs/fidfab•00 pull requests in fideus-labs/fidfab•Updated Nov 13, 2026Nov 13, 2026

• KonfAI

  Public
  KonfAI: the declarative engine for medical-imaging AI. Train from one YAML, inspect with Scout, benchmark on FidOpt, ship to 3D Slicer, agents and the browser.

  deep-learningmcppytorch+ 7

  deep-learningmcppytorchmedical-imagingsegmentationreproducibilityimage-registration3d-slicerimage-synthesisome-zarr

  Python

  •

  Apache License 2.0

  •33 forks in fideus-labs/KonfAI•1717 stars in fideus-labs/KonfAI•00 issues in fideus-labs/KonfAI•77 pull requests in fideus-labs/KonfAI•Updated Nov 13, 2026Nov 13, 2026

• ngff-zarr

  Public
  A lean and kind Open Microscopy Environment (OME) Next Generation File Format (NGFF) Zarr implementation.

  pythonmedicaldask+ 4

  pythonmedicaldaskmicroscopyimagingome-zarrome-zarr-converter

  Python

  •

  MIT License

  •2727 forks in fideus-labs/ngff-zarr•7575 stars in fideus-labs/ngff-zarr•1313 issues in fideus-labs/ngff-zarr•1111 pull requests in fideus-labs/ngff-zarr•Updated Nov 13, 2026Nov 13, 2026

• SlicerOMEZarr

  Public
  3D Slicer extension to open OME-Zarr (OME-NGFF) images, built on ngff-zarr

  3d-slicer-extension

  3d-slicer-extension

  Python

  •

  MIT License

  •11 fork in fideus-labs/SlicerOMEZarr•33 stars in fideus-labs/SlicerOMEZarr•11 issue in fideus-labs/SlicerOMEZarr•11 pull request in fideus-labs/SlicerOMEZarr•Updated Nov 11, 2026Nov 11, 2026

• python-wasm-parallelism

  Public
  Parallel processing in Pyodide/Jupyterlite with Dask or multiprocessing

  pythonmultiprocessingwebassembly+ 6

  pythonmultiprocessingwebassemblywasmparallelismdaskwebworkerspyodidejupyterlite

  TypeScript

  •

  MIT License

  •00 forks in fideus-labs/python-wasm-parallelism•66 stars in fideus-labs/python-wasm-parallelism•00 issues in fideus-labs/python-wasm-parallelism•00 pull requests in fideus-labs/python-wasm-parallelism•Updated Nov 6, 2026Nov 6, 2026

• ome-zarr-registration-tutorial

  Public
  Out-of-core registration, OME-Zarr in and out: a four-step tutorial (read, register, write, apply)

  tutorialitkmicroscopy+ 6

  tutorialitkmicroscopyimage-registrationout-of-core3d-slicernaparingffome-zarr

  Jupyter Notebook

  •

  MIT License

  •00 forks in fideus-labs/ome-zarr-registration-tutorial•66 stars in fideus-labs/ome-zarr-registration-tutorial•00 issues in fideus-labs/ome-zarr-registration-tutorial•00 pull requests in fideus-labs/ome-zarr-registration-tutorial•Updated Nov 6, 2026Nov 6, 2026

• nd-image-codecs

  Public
  Composable Zarr v3 codecs for ND scientific images.

  Rust

  •

  MIT License

  •11 fork in fideus-labs/nd-image-codecs•66 stars in fideus-labs/nd-image-codecs•77 issues in fideus-labs/nd-image-codecs•22 pull requests in fideus-labs/nd-image-codecs•Updated Oct 19, 2026Oct 19, 2026

• fiff

  Public
  Present TIFF files as a zarrita.js Zarr store following the NGFF OME-Zarr data model

  javascripttypescripttiff+ 3

  javascripttypescripttiffngffome-zarrome-ngff

  TypeScript

  •

  MIT License

  •00 forks in fideus-labs/fiff•44 stars in fideus-labs/fiff•11 issue in fideus-labs/fiff•00 pull requests in fideus-labs/fiff•Updated Oct 8, 2026Oct 8, 2026

• worker-pool

  Public
  A Web Worker pool with bounded concurrency, plus a companion package that accelerates zarrita codec operations on Web Workers.

  javascripttypescriptweb-worker+ 4

  javascripttypescriptweb-workerthread-poolzarrp-queueitk-wasm

  TypeScript

  •

  MIT License

  •22 forks in fideus-labs/worker-pool•55 stars in fideus-labs/worker-pool•00 issues in fideus-labs/worker-pool•00 pull requests in fideus-labs/worker-pool•Updated Sep 30, 2026Sep 30, 2026

• impact-reg-ooc-demo

  Public
  Out-of-core multimodal registration with KonfAI and impact-reg: elastix, FireANTs, ConvexAdam and IMPACT feature losses on the APEX / BRAIN CONNECTS hackathon d…

  neuroscienceregistrationneuroimaging+ 5

  neuroscienceregistrationneuroimagingout-of-coremultimodalneuroglancerfsleyesome-zarr

  Python

  •00 forks in fideus-labs/impact-reg-ooc-demo•11 star in fideus-labs/impact-reg-ooc-demo•00 issues in fideus-labs/impact-reg-ooc-demo•00 pull requests in fideus-labs/impact-reg-ooc-demo•Updated Sep 16, 2026Sep 16, 2026

• ImpactLoss

  Public
  IMPACT Reg: A Generic Semantic Loss for Multimodal Image Registration

  Python

  •

  Apache License 2.0

  •22 forks in fideus-labs/ImpactLoss•00 stars in fideus-labs/ImpactLoss•00 issues in fideus-labs/ImpactLoss•11 pull request in fideus-labs/ImpactLoss•Updated Sep 8, 2026Sep 8, 2026

• rumcodecs

  Public archive
  numcodecs.js reimplemented in Rust

  rustwebassemblyzarr+ 1

  rustwebassemblyzarrnumcodecs

  TypeScript

  •

  MIT License

  •00 forks in fideus-labs/rumcodecs•22 stars in fideus-labs/rumcodecs•00 issues in fideus-labs/rumcodecs•00 pull requests in fideus-labs/rumcodecs•Updated Aug 7, 2026Aug 7, 2026

• ome-zarr-rfc4-validation

  Public
  OME-NGFF RFC-4 (axis anatomical orientation) validator + conformance suite. Data: HF fideus-labs/ome-ngff-rfc4-orientation-validation.

  Python

  •00 forks in fideus-labs/ome-zarr-rfc4-validation•33 stars in fideus-labs/ome-zarr-rfc4-validation•00 issues in fideus-labs/ome-zarr-rfc4-validation•00 pull requests in fideus-labs/ome-zarr-rfc4-validation•Updated Aug 4, 2026Aug 4, 2026

• fidnii

  Public
  Render OME-Zarr images in NiiVue with progressive multi-resolution loading.

  TypeScript

  •

  MIT License

  •11 fork in fideus-labs/fidnii•99 stars in fideus-labs/fidnii•3636 issues in fideus-labs/fidnii•44 pull requests in fideus-labs/fidnii•Updated Jun 25, 2026Jun 25, 2026

• numcodecs.js

  Public
  Buffer compression and transformation codecs

  JavaScript

  •

  MIT License

  •1010 forks in fideus-labs/numcodecs.js•00 stars in fideus-labs/numcodecs.js•00 issues in fideus-labs/numcodecs.js•00 pull requests in fideus-labs/numcodecs.js•Updated Feb 25, 2026Feb 25, 2026

• ome-ngff-scientific-ai

  Public
  Scientific AI and the Future of OME-NGFF: Intelligent Bioimage Analysis Workflows

  bioimage-analysisbioimage-toolsscientific-ai+ 2

  bioimage-analysisbioimage-toolsscientific-aiome-zarrome-ngff

  Dockerfile

  •

  MIT License

  •00 forks in fideus-labs/ome-ngff-scientific-ai•22 stars in fideus-labs/ome-ngff-scientific-ai•00 issues in fideus-labs/ome-ngff-scientific-ai•00 pull requests in fideus-labs/ome-ngff-scientific-ai•Updated Nov 11, 2025Nov 11, 2025

• .github

  Public
  MIT License

  •00 forks in fideus-labs/.github•00 stars in fideus-labs/.github•00 issues in fideus-labs/.github•00 pull requests in fideus-labs/.github•Updated Sep 19, 2025Sep 19, 2025

• scientific-ai-omezarr-tutorial

  Public
  Scientific AI and the Future of OME-Zarr: Building Intelligent Bioimage Analysis Workflows

  bioimagingbioimage-analysiszarr+ 3

  bioimagingbioimage-analysiszarrscientific-aiome-zarrmcp-server

  Dockerfile

  •

  MIT License

  •11 fork in fideus-labs/scientific-ai-omezarr-tutorial•33 stars in fideus-labs/scientific-ai-omezarr-tutorial•00 issues in fideus-labs/scientific-ai-omezarr-tutorial•00 pull requests in fideus-labs/scientific-ai-omezarr-tutorial•Updated Sep 18, 2025Sep 18, 2025