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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 23

  2. BigStitcher BigStitcher Public

    ImgLib2/BDV implementation of Stitching for large datasets

    Java 80 17

  3. JRCLUST JRCLUST Public

    JRCLUST

    MATLAB 35 22

  4. multifish multifish Public

    EASI-FISH analysis pipeline for spatial transcriptomics

    Jupyter Notebook 34 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 315 repositories
  • fileglancer Public

    Browse, share, and publish OME-Zarr data

    JaneliaSciComp/fileglancer’s past year of commit activity
    TypeScript 19 BSD-3-Clause 4 0 6 Updated Mar 18, 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 3 8 0 Updated Mar 18, 2026
  • ephys-pipeline Public

    Pipeline to process electrophysiology data.

    JaneliaSciComp/ephys-pipeline’s past year of commit activity
    Python 0 0 6 0 Updated Mar 18, 2026
  • claude-howto Public
    JaneliaSciComp/claude-howto’s past year of commit activity
    Shell 3 0 0 0 Updated Mar 18, 2026
  • workstation Public

    Janelia Workstation

    JaneliaSciComp/workstation’s past year of commit activity
    Java 26 12 1 12 Updated Mar 18, 2026
  • easifish Public
    JaneliaSciComp/easifish’s past year of commit activity
    Nextflow 1 BSD-3-Clause 0 0 0 Updated Mar 18, 2026
  • BigStitcher-Spark Public

    Running compute-intense parts of BigStitcher distributed

    JaneliaSciComp/BigStitcher-Spark’s past year of commit activity
    Java 30 BSD-2-Clause 17 19 3 Updated Mar 18, 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 Mar 18, 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 Mar 18, 2026
  • videoAnnotation Public
    JaneliaSciComp/videoAnnotation’s past year of commit activity
    JavaScript 2 BSD-3-Clause 0 0 0 Updated Mar 18, 2026
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