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@royerlab Royer Lab at CZB SF

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    43 repositories

    • ultrack

      Public
      Cell tracking and segmentation software
      gurobicell-segmentationcell-trackingcell-tracking-challenge
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •11•87•41•3•Updated Oct 2, 2024Oct 2, 2024

    • softcopy

      Public
      Copies zarr archives from an acquisition frontend to a different disk, using filesystem watching and lockfiles to allow copying during acquisition
      Python
      •0•0•0•0•Updated Sep 30, 2024Sep 30, 2024

    • ssi-code

      Public
      Image Deconvolution via Noise-Tolerant Self-Supervised Inversion
      pythondenoise-imagesdeconvolve
      Python
      •10•28•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
      •2•20•1•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

    • dexpv2

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•1•0•Updated Sep 14, 2024Sep 14, 2024

    • in-silico-fate-mapping

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•6•1•1•Updated Sep 14, 2024Sep 14, 2024

    • daxi

      Public
      High-Resolution, Large Field-of-View, and Multi-ViewSingle Objective Light-Sheet Microscopy
      Python
      •
      Other
      •2•25•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-napari-animation

      Public
      Zebrahub's napari-animation demo
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•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•1•0•0•Updated Sep 13, 2024Sep 13, 2024

    • zebrahub-paper-umap-3d

      Public
      Generate 3D UMAPs of zebrafish
      Python
      •
      MIT License
      •1•4•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•73•7•1•Updated Sep 13, 2024Sep 13, 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
      •0•3•3•0•Updated Sep 6, 2024Sep 6, 2024

    • napari-chatgpt

      Public
      A napari plugin to process and analyse images with chatGPT!
      CSS
      •
      BSD 3-Clause "New" or "Revised" License
      •25•238•8•0•Updated Aug 31, 2024Aug 31, 2024

    • napari-segment-anything

      Public
      Segment Anything Model (SAM) native Qt UI
      Python
      •
      Apache License 2.0
      •17•190•13•2•Updated Aug 29, 2024Aug 29, 2024

    • slurmkit

      Public
      Simple SLURM python API
      Python
      •
      MIT License
      •1•7•0•0•Updated Aug 23, 2024Aug 23, 2024

    • ultrack-imagej

      Public
      Java
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Aug 8, 2024Aug 8, 2024

    • ultrack-i2k2023

      Public
      Ultrack https://github.com/royerlab/ultrack from Images to Knowledge - 2023 workshop
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•2•0•0•Updated Jun 8, 2024Jun 8, 2024

    • imagej.github.io

      Public
      The ImageJ wiki
      JavaScript
      •
      Other
      •116•0•0•0•Updated May 22, 2024May 22, 2024

    • .github

      Public
      0•0•0•0•Updated Apr 17, 2024Apr 17, 2024

    • preprints

      Public
      All Royer lab preprints can be found here
      0•0•0•0•Updated Jul 17, 2023Jul 17, 2023

    • dexp

      Public
      Dataset EXploration & Processing
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •6•29•10•0•Updated May 11, 2023May 11, 2023

    • aydin

      Public
      Aydin — User-friendly, Fast, Self-Supervised Image Denoising for All.
      pythonimageneural-networkimage-processingdenoisingmachine-learningdeep-learning
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •14•149•17•13•Updated Apr 14, 2023Apr 14, 2023

    • daxi-controller

      Public
      HTML
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Feb 24, 2023Feb 24, 2023

    • napari-umap

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•2•0•0•Updated Nov 1, 2022Nov 1, 2022

    • ZAF

      Public
      ZAF(Zebrafish Automated Feeder): Software needed for automated fish feeding system of our fish facility
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•4•1•1•Updated Aug 25, 2022Aug 25, 2022

    • napari-aydin

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•3•0•Updated Aug 1, 2022Aug 1, 2022

    • napari-3D-rotation

      Public
      Generate rotating 3D UMAP in napari
      Python
      •
      MIT License
      •1•0•0•0•Updated Jul 29, 2022Jul 29, 2022