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@royerlab Royer Lab at CZB SF

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    54 repositories

    • tracksdata

      Public
      A common data structure and basic tools for multi-object tracking.
      trackingmulti-object-trackingcell-trackingcell-tracking-challenge
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•1•4•3•Updated Jul 15, 2025Jul 15, 2025

    • inTRACKtive

      Public
      Interactive visualization and sharing of cell tracking data in the browser
      TypeScript
      •
      MIT License
      •1•28•19•8•Updated Jul 15, 2025Jul 15, 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

    • ultrack

      Public
      Cell tracking and segmentation software
      gurobicell-segmentationcell-trackingcell-tracking-challenge
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •18•122•54•4•Updated Jul 11, 2025Jul 11, 2025

    • trackedit

      Public
      Interactive tracks editing tool for Ultrack
      Python
      •
      MIT License
      •1•5•10•1•Updated Jul 11, 2025Jul 11, 2025

    • 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 interacting with Large Language Models (LLMs) from various providers, along with a powerful agentic AI framework that supports multimodal inputs and outputs.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•17•0•1•Updated Jul 3, 2025Jul 3, 2025

    • napari-chatgpt

      Public
      A napari plugin to process and analyse images with chatGPT!
      CSS
      •
      BSD 3-Clause "New" or "Revised" License
      •29•277•13•1•Updated Jun 28, 2025Jun 28, 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•3•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

    • arbol

      Public
      arbol - Arborescent Printouts in Python
      Python
      •
      MIT License
      •0•6•0•0•Updated Mar 4, 2025Mar 4, 2025

    • in-silico-fate-mapping

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•7•1•1•Updated Feb 14, 2025Feb 14, 2025

    • ultrack_supplementary

      Public
      Python
      •0•0•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•4•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

    • napari-segment-anything-2

      Public
      Native Qt interface for Meta's Segment Anything 2 in Images and Videos
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•28•5•0•Updated Sep 26, 2024Sep 26, 2024

    • opensimview

      Public
      New ClearControl + Dorado +.... combined repo
      Java
      •1•1•0•0•Updated Sep 23, 2024Sep 23, 2024

    • daxi

      Public
      High-Resolution, Large Field-of-View, and Multi-ViewSingle Objective Light-Sheet Microscopy
      Python
      •
      Other
      •2•27•1•0•Updated Sep 14, 2024Sep 14, 2024

    • napari-dexp

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•0•0•1•Updated Sep 13, 2024Sep 13, 2024

    • zebrahub-paper-hcr-analysis

      Public
      Scripts for analyzing HCR data for zebrafish tail.
      Python
      •0•0•0•0•Updated Sep 13, 2024Sep 13, 2024

    • zebrahub-protocols

      Public
      Creative Commons Zero v1.0 Universal
      •0•2•0•0•Updated Sep 13, 2024Sep 13, 2024

    • zebrahub-paper-umap-3d

      Public
      Generate 3D UMAPs of zebrafish
      Python
      •
      MIT License
      •2•7•0•0•Updated Sep 13, 2024Sep 13, 2024

    • cytoself

      Public
      Self-supervised models for encoding protein localization patterns from microscopy images
      pytorchproteinautoencoderfluorescencemicroscopyimagingself-supervisedself-supervised-learningopencelldeep-learning
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •15•76•8•1•Updated Sep 13, 2024Sep 13, 2024
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