Repositories list

• aydin

  Public
  Aydin — User-friendly, Fast, Self-Supervised Image Denoising for All.

  pythonmachine-learningimage+ 4deep-learningneural-networkimage-processingdenoising

  Python

  •

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

  •14•172•2•0•Updated Feb 16, 2026Feb 16, 2026

• litemind

  Public
  litemind is a Python library designed to empower developers to build sophisticated conversational agents and tools. It provides a flexible and elegant API for i…

  Python

  •

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

  •3•18•0•0•Updated Feb 14, 2026Feb 14, 2026

• napari-chatgpt

  Public
  A napari plugin to process and analyse images with chatGPT!

  Python

  •

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

  •32•284•0•3•Updated Feb 14, 2026Feb 14, 2026

• trackedit

  Public
  Interactive tracks editing tool for Ultrack

  Python

  •

  MIT License

  •1•6•11•3•Updated Feb 14, 2026Feb 14, 2026

• tracksdata

  Public
  A common data structure and basic tools for multi-object tracking.

  trackingmulti-object-trackingcell-tracking+ 1cell-tracking-challenge

  Python

  •

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

  •4•9•24•8•Updated Feb 12, 2026Feb 12, 2026

• ops_model

  Public
  Python

  •

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

  •0•1•2•4•Updated Feb 12, 2026Feb 12, 2026

• ultrack

  Public
  Cell tracking and segmentation software

  gurobicell-segmentationcell-tracking+ 1cell-tracking-challenge

  Python

  •

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

  •24•170•63•6•Updated Feb 11, 2026Feb 11, 2026

• ultrack-td

  Public
  Tracksdata compatible ultrack package

  C++

  •

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

  •0•3•0•0•Updated Feb 4, 2026Feb 4, 2026

• arbol

  Public
  arbol - Arborescent Printouts in Python

  Python

  •

  MIT License

  •0•8•0•0•Updated Feb 1, 2026Feb 1, 2026

• cuws

  Public
  CuWS implements watershed segmentation from minima on GPUs

  Python

  •0•2•0•0•Updated Jan 30, 2026Jan 30, 2026

• inTRACKtive

  Public
  Interactive visualization and sharing of cell tracking data in the browser

  TypeScript

  •

  MIT License

  •6•45•22•9•Updated Dec 16, 2025Dec 16, 2025

• contrastive-td

  Public
  A toolbox for contrastive learning on tracksdata graphs.

  Python

  •

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

  •0•0•0•0•Updated Dec 11, 2025Dec 11, 2025

• img-embed-td

  Public
  A toolbox for image embedding feature extraction for tracksdata & geff graphs.

  Python

  •

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

  •0•0•1•0•Updated Nov 17, 2025Nov 17, 2025

• in-silico-fate-mapping

  Public
  Python

  •

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

  •1•7•1•1•Updated Nov 5, 2025Nov 5, 2025

• napari-mcp

  Public
  🔬 MCP server for AI-powered napari control. Connect Claude, ChatGPT, Cursor, and other LLMs to napari for interactive image analysis. Perfect for automating mic…

  mcpmicroscopynapari-plugin+ 4naparillmclaude-desktopfastmcp

  Python

  •

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

  •2•17•0•0•Updated Sep 30, 2025Sep 30, 2025

• cytoself

  Public
  Self-supervised models for encoding protein localization patterns from microscopy images

  deep-learningtensorflowpytorch+ 8proteinautoencoderfluorescencemicroscopyimagingself-supervisedself-supervised-learning+ 1

  Python

  •

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

  •16•80•8•1•Updated Aug 5, 2025Aug 5, 2025

• softcopy

  Public
  Copies zarr archives from an acquisition frontend to a different disk, using filesystem watching and lockfiles to allow copying during acquisition

  Python

  •

  MIT License

  •0•0•8•0•Updated Jul 14, 2025Jul 14, 2025

• zebrahub-napari-animation

  Public
  Zebrahub's napari-animation demo

  Python

  •

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

  •0•1•0•0•Updated Jun 2, 2025Jun 2, 2025

• power_daemon

  Public
  Python

  •0•0•0•0•Updated May 19, 2025May 19, 2025

• dexpv2

  Public
  Python

  •

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

  •0•4•1•1•Updated May 9, 2025May 9, 2025

• ultrack-atini-2025

  Public
  Ultrack's hands-on exercise for Advanced Techniques in NeuroImaging (ATiNI) 2025

  cell-segmentationcell-trackingcell-tracking-challenge

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

  •0•0•0•0•Updated May 2, 2025May 2, 2025

• .github

  Public
  0•0•0•0•Updated Mar 4, 2025Mar 4, 2025

• ultrack_supplementary

  Public
  Python

  •0•2•0•0•Updated Feb 5, 2025Feb 5, 2025

• ultrack-i2k2024

  Public
  Ultrack From Images to Knowledge (I2k) 2024 Workshop

  cell-trackingcell-tracking-challengeultrack

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

  •1•4•0•0•Updated Jan 13, 2025Jan 13, 2025

• ultrack_CTC_submission

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Jan 10, 2025Jan 10, 2025

• python-mip-feedstock

  Public
  Shell

  •

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

  •0•0•0•0•Updated Dec 19, 2024Dec 19, 2024

• czpeedy

  Public
  A tool for experimentally determining the best tensorstore spec for a given machine and dataset.

  Python

  •

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

  •1•5•3•0•Updated Dec 11, 2024Dec 11, 2024

• napari-royerlab-data

  Public
  Python

  •

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

  •0•1•0•0•Updated Oct 11, 2024Oct 11, 2024

• slurmkit

  Public
  Simple SLURM python API

  Python

  •

  MIT License

  •1•9•0•0•Updated Oct 10, 2024Oct 10, 2024

• ssi-code

  Public
  Image Deconvolution via Noise-Tolerant Self-Supervised Inversion

  pythondenoise-imagesdeconvolve

  Python

  •10•30•2•3•Updated Sep 30, 2024Sep 30, 2024