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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
  • 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
  • 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
  • mia-snippets Public
    JaneliaSciComp/mia-snippets's past year of commit activity
    Python 0 0 0 0 Updated Oct 28, 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 Oct 28, 2026
  • containers Public

    Containers for workflow plugins

    JaneliaSciComp/containers's past year of commit activity
    Python 0 BSD-3-Clause 0 0 1 Updated Oct 28, 2026
  • beyene-lab Public
    JaneliaSciComp/beyene-lab's past year of commit activity
    MATLAB 0 BSD-3-Clause 0 0 1 Updated Oct 27, 2026
  • fileglancer Public

    Browse, share, and publish OME-Zarr data

    JaneliaSciComp/fileglancer's past year of commit activity
    TypeScript 30 BSD-3-Clause 5 2 6 Updated Oct 27, 2026
  • chunkmirage Public

    Serve virtual chunked arrays (Zarr, N5, precomputed) over HTTP: each chunk computed on request by a pipeline you can edit live.

    JaneliaSciComp/chunkmirage's past year of commit activity
    Python 3 BSD-3-Clause 0 0 1 Updated Oct 27, 2026
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