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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 361 repositories
  • fileglancer Public

    Browse, share, and publish OME-Zarr data

    JaneliaSciComp/fileglancer's past year of commit activity
    TypeScript 30 BSD-3-Clause 5 2 7 Updated Oct 28, 2026
  • VVDViewer Public

    3D/4D volumetric rendering of microscopy data

    JaneliaSciComp/VVDViewer's past year of commit activity
    C++ 28 BSD-3-Clause 6 4 5 Updated Oct 28, 2026
  • neuronbridge-services Public

    AWS Services for NeuronBridge

    JaneliaSciComp/neuronbridge-services's past year of commit activity
    JavaScript 2 BSD-3-Clause 2 0 19 Updated Oct 28, 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 28, 2026
  • exllsm-circuit-reconstruction Public

    Nextflow pipeline encapsulating workflows for analyzing expansion lattice light-sheet microscopy (ExLLSM) imagery

    JaneliaSciComp/exllsm-circuit-reconstruction's past year of commit activity
    Nextflow 13 BSD-3-Clause 1 2 0 Updated Oct 28, 2026
  • mia-workflow-prototype Public
    JaneliaSciComp/mia-workflow-prototype's past year of commit activity
    Python 0 0 7 1 Updated Oct 28, 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 28, 2026
  • BigStitcher-Spark Public

    Running compute-intense parts of BigStitcher distributed

    JaneliaSciComp/BigStitcher-Spark's past year of commit activity
    Java 32 BSD-2-Clause 20 19 2 Updated Oct 28, 2026
  • h5j-ng-viewer Public

    Browser-only H5J to OME-Zarr to Neuroglancer viewer. No backend, no upload.

    JaneliaSciComp/h5j-ng-viewer's past year of commit activity
    TypeScript 0 0 0 0 Updated Oct 28, 2026
  • janelia-jhdf5 Public

    SciJava JHDF5 from Janelia

    JaneliaSciComp/janelia-jhdf5's past year of commit activity
    Java 1 Apache-2.0 1 0 0 Updated Oct 28, 2026
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