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@JaneliaSciComp

Howard Hughes Medical Institute

GitHub organization maintained by Scientific Computing Software at HHMI's Janelia Research Campus for use by HHMI staff and external collaborators.

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  1. bigstream bigstream Public

    Tools for distributed alignment of massive images

    Jupyter Notebook 93 22

  2. BigStitcher BigStitcher Public

    ImgLib2/BDV implementation of Stitching for large datasets

    Java 79 17

  3. JRCLUST JRCLUST Public

    JRCLUST

    MATLAB 35 22

  4. multifish multifish Public

    EASI-FISH analysis pipeline for spatial transcriptomics

    Jupyter Notebook 35 13

  5. multiview-reconstruction multiview-reconstruction Public

    Software for the reconstruction of multi-view microscopic acquisitions like Selective Plane Illumination Microscopy (SPIM) Data

    Java 32 24

  6. BigStitcher-Spark BigStitcher-Spark Public

    Running compute-intense parts of BigStitcher distributed

    Java 30 17

Repositories

Showing 10 of 311 repositories
  • fileglancer Public

    Browse, share, and publish OME-Zarr data

    JaneliaSciComp/fileglancer’s past year of commit activity
    TypeScript 19 BSD-3-Clause 2 0 6 Updated Feb 13, 2026
  • py-cluster-api Public

    Python API for HPC clusters

    JaneliaSciComp/py-cluster-api’s past year of commit activity
    Python 0 BSD-3-Clause 0 0 0 Updated Feb 13, 2026
  • decode_fish_2026 Public Forked from TuragaLab/decode_fish
    JaneliaSciComp/decode_fish_2026’s past year of commit activity
    Jupyter Notebook 0 Apache-2.0 2 0 0 Updated Feb 13, 2026
  • janelia-unity-toolkit Public

    Packages for the Unity game engine, emphasizing animal studies in VR.

    JaneliaSciComp/janelia-unity-toolkit’s past year of commit activity
    C# 18 12 7 3 Updated Feb 13, 2026
  • fileglancer-demo-app Public
    JaneliaSciComp/fileglancer-demo-app’s past year of commit activity
    Python 0 BSD-3-Clause 0 0 0 Updated Feb 13, 2026
  • multiview-reconstruction Public

    Software for the reconstruction of multi-view microscopic acquisitions like Selective Plane Illumination Microscopy (SPIM) Data

    JaneliaSciComp/multiview-reconstruction’s past year of commit activity
    Java 32 GPL-2.0 24 30 7 Updated Feb 13, 2026
  • bigstream Public

    Tools for distributed alignment of massive images

    JaneliaSciComp/bigstream’s past year of commit activity
    Jupyter Notebook 93 BSD-3-Clause 22 13 3 Updated Feb 13, 2026
  • neuronbridge-aligners Public

    Containerized Brain/VNC aligners for NeuronBridge

    JaneliaSciComp/neuronbridge-aligners’s past year of commit activity
    ImageJ Macro 1 BSD-3-Clause 0 0 0 Updated Feb 12, 2026
  • tensorswitch Public

    This package provides a unified entry point and organized task modules for managing N5/Zarr dataset conversions and downsampling. It centralizes your workflow into a single pipeline to reduce manual work and errors.

    JaneliaSciComp/tensorswitch’s past year of commit activity
    Python 3 BSD-3-Clause 0 0 0 Updated Feb 12, 2026
  • ReiserFlyDiscoSettings Public

    Settings folder for Reiser Lab

    JaneliaSciComp/ReiserFlyDiscoSettings’s past year of commit activity
    Shell 0 0 0 0 Updated Feb 12, 2026
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