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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 95 25

  2. BigStitcher BigStitcher Public

    ImgLib2/BDV implementation of Stitching for large datasets

    Java 84 17

  3. RS-FISH RS-FISH Public

    Tool for precise, interactive, fast and scalable FISH spot detection

    Java 55 15

  4. multifish multifish Public

    EASI-FISH analysis pipeline for spatial transcriptomics

    Jupyter Notebook 36 13

  5. JRCLUST JRCLUST Public

    JRCLUST

    MATLAB 35 23

  6. multiview-reconstruction multiview-reconstruction Public

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

    Java 35 26

Repositories

Showing 10 of 357 repositories
  • neuronbridge-precompute Public

    Utilities for indexing and transferring of NeuronBridge-related files

    JaneliaSciComp/neuronbridge-precompute's past year of commit activity
    Python 0 BSD-3-Clause 0 0 0 Updated Oct 6, 2026
  • rnanix_server_frontend Public
    JaneliaSciComp/rnanix_server_frontend's past year of commit activity
    JavaScript 0 1 0 1 Updated Oct 6, 2026
  • jacs-model Public

    JACS Domain Model and DAOs

    JaneliaSciComp/jacs-model's past year of commit activity
    Java 1 BSD-3-Clause 0 0 1 Updated Oct 6, 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# 19 13 9 7 Updated Oct 6, 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 35 GPL-2.0 26 33 5 Updated Oct 6, 2026
  • habitat_pipeline Public

    Integrated Multi-Animal Electrophysiology and Behavior Analysis Pipeline

    JaneliaSciComp/habitat_pipeline's past year of commit activity
    Jupyter Notebook 0 0 0 0 Updated Oct 6, 2026
  • janelia-jhdf5 Public

    SciJava JHDF5 from Janelia

    JaneliaSciComp/janelia-jhdf5's past year of commit activity
    Java 1 0 0 12 Updated Oct 6, 2026
  • jacs-compute Public

    JAnelia Compute Services (JACS)

    JaneliaSciComp/jacs-compute's past year of commit activity
    Java 1 BSD-3-Clause 0 0 0 Updated Oct 5, 2026
  • rna_atlas_website Public
    JaneliaSciComp/rna_atlas_website's past year of commit activity
    Python 0 0 0 0 Updated Oct 5, 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 7 BSD-3-Clause 5 0 0 Updated Oct 5, 2026
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