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@royerlab Royer Lab at Biohub SF

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    60 repositories

    • inTRACKtive

      Public
      Interactive visualization and sharing of cell tracking data in the browser
      TypeScript
      •
      MIT License
      •6•46•22•9•Updated Apr 9, 2026Apr 9, 2026

    • ops_model

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•2•5•Updated Apr 8, 2026Apr 8, 2026

    • ultrack-td

      Public
      Tracksdata compatible ultrack package
      C++
      •
      BSD 3-Clause "New" or "Revised" License
      •0•3•0•1•Updated Apr 6, 2026Apr 6, 2026

    • tracksdata

      Public
      A common data structure and basic tools for multi-object tracking.
      trackingmulti-object-trackingcell-tracking
      trackingmulti-object-trackingcell-trackingcell-tracking-challenge
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •5•9•22•8•Updated Apr 6, 2026Apr 6, 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
      •4•18•0•0•Updated Apr 5, 2026Apr 5, 2026

    • cuws

      Public
      CuWS implements watershed segmentation from minima on GPUs
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•4•0•0•Updated Apr 1, 2026Apr 1, 2026

    • dexpv2

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•4•1•1•Updated Apr 1, 2026Apr 1, 2026

    • ultrack

      Public
      Cell tracking and segmentation software
      gurobicell-segmentationcell-tracking
      gurobicell-segmentationcell-trackingcell-tracking-challenge
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •25•174•65•4•Updated Apr 1, 2026Apr 1, 2026

    • trackedit

      Public
      Interactive tracks editing tool for Ultrack
      Python
      •
      MIT License
      •2•6•11•2•Updated Mar 25, 2026Mar 25, 2026

    • 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
      mcpmicroscopynapari-pluginnaparillmclaude-desktopfastmcp
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •6•31•1•1•Updated Mar 25, 2026Mar 25, 2026

    • aydin

      Public
      Aydin — User-friendly, Fast, Self-Supervised Image Denoising for All.
      pythonmachine-learningimage
      pythonmachine-learningimagedeep-learningneural-networkimage-processingdenoising
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •14•173•3•1•Updated Feb 22, 2026Feb 22, 2026

    • arbol

      Public
      arbol - Arborescent Printouts in Python
      Python
      •
      MIT License
      •0•8•0•0•Updated Feb 22, 2026Feb 22, 2026

    • napari-chatgpt

      Public
      A napari plugin to process and analyse images with chatGPT!
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •32•293•0•3•Updated Feb 14, 2026Feb 14, 2026

    • 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

    • cytoself

      Public
      Self-supervised models for encoding protein localization patterns from microscopy images
      deep-learningtensorflowpytorch
      deep-learningtensorflowpytorchproteinautoencoderfluorescencemicroscopyimagingself-supervisedself-supervised-learning
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •16•84•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

    • ultrack-atini-2025

      Public
      Ultrack's hands-on exercise for Advanced Techniques in NeuroImaging (ATiNI) 2025
      cell-segmentationcell-trackingcell-tracking-challenge
      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
      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
      pythondenoise-imagesdeconvolve
      Python
      •10•30•2•3•Updated Sep 30, 2024Sep 30, 2024
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