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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 91 22

  2. BigStitcher BigStitcher Public

    ImgLib2/BDV implementation of Stitching for large datasets

    Java 78 17

  3. NIDAQ.jl NIDAQ.jl Public

    National Instruments Data Acquisition Interface

    Julia 49 16

  4. JRCLUST JRCLUST Public

    JRCLUST

    MATLAB 35 22

  5. multifish multifish Public

    EASI-FISH analysis pipeline for spatial transcriptomics

    Jupyter Notebook 35 13

  6. multiview-reconstruction multiview-reconstruction Public

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

    Java 31 24

Repositories

Showing 10 of 303 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 Jan 10, 2026
  • easifish Public
    JaneliaSciComp/easifish’s past year of commit activity
    Nextflow 1 BSD-3-Clause 0 0 0 Updated Jan 10, 2026
  • bigstream Public

    Tools for distributed alignment of massive images

    JaneliaSciComp/bigstream’s past year of commit activity
    Jupyter Notebook 91 BSD-3-Clause 22 13 3 Updated Jan 10, 2026
  • neuronbridge-python Public

    Python API for NeuronBridge

    JaneliaSciComp/neuronbridge-python’s past year of commit activity
    Jupyter Notebook 0 BSD-3-Clause 0 1 0 Updated Jan 10, 2026
  • claude-howto Public
    JaneliaSciComp/claude-howto’s past year of commit activity
    Shell 1 0 0 0 Updated Jan 9, 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 31 GPL-2.0 24 29 6 Updated Jan 9, 2026
  • fileglancer Public

    Browse, share, and publish OME-Zarr data

    JaneliaSciComp/fileglancer’s past year of commit activity
    TypeScript 17 BSD-3-Clause 2 2 6 Updated Jan 9, 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 11 6 2 Updated Jan 9, 2026
  • SOFIMA-scripts Public

    wrapper to batch jobs to cluster

    JaneliaSciComp/SOFIMA-scripts’s past year of commit activity
    Python 1 BSD-3-Clause 1 0 0 Updated Jan 9, 2026
  • EM_recon_pipeline Public

    Pipeline scripts and tools for reconstructing Electron Microscopy volumes.

    JaneliaSciComp/EM_recon_pipeline’s past year of commit activity
    Python 3 BSD-3-Clause 3 0 5 Updated Jan 9, 2026
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