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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 365 repositories
  • 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 6 Updated Nov 14, 2026
  • mia-workflows Public
    JaneliaSciComp/mia-workflows's past year of commit activity
    Python 0 0 7 1 Updated Nov 14, 2026
  • mia-snippets Public
    JaneliaSciComp/mia-snippets's past year of commit activity
    Python 0 0 6 5 Updated Nov 14, 2026
  • ossi-website Public

    Website showcasing Janelia Open Science Software Intiative (OSSI) supported software projects and other software developed at Janelia.

    JaneliaSciComp/ossi-website's past year of commit activity
    JavaScript 3 BSD-3-Clause 21 16 1 Updated Nov 13, 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 3 Updated Nov 13, 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 5 BSD-3-Clause 3 0 8 Updated Nov 13, 2026
  • BigStitcher Public

    ImgLib2/BDV implementation of Stitching for large datasets

    JaneliaSciComp/BigStitcher's past year of commit activity
    Java 84 GPL-2.0 17 92 2 Updated Nov 13, 2026
  • triton-sam2 Public

    SAM2 deployed with Triton Inference Server

    JaneliaSciComp/triton-sam2's past year of commit activity
    Python 4 1 0 0 Updated Nov 13, 2026
  • fileglancer Public

    Browse, share, and publish OME-Zarr data

    JaneliaSciComp/fileglancer's past year of commit activity
    TypeScript 33 BSD-3-Clause 5 1 7 Updated Nov 13, 2026
  • rna-cryoem-data-portal Public
    JaneliaSciComp/rna-cryoem-data-portal's past year of commit activity
    Python 0 0 0 0 Updated Nov 13, 2026
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