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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 351 repositories
  • BigStitcher-Spark Public

    Running compute-intense parts of BigStitcher distributed

    JaneliaSciComp/BigStitcher-Spark's past year of commit activity
    Java 30 BSD-2-Clause 20 19 2 Updated Sep 22, 2026
  • bigstream Public

    Tools for distributed alignment of massive images

    JaneliaSciComp/bigstream's past year of commit activity
    Jupyter Notebook 95 BSD-3-Clause 25 13 3 Updated Sep 21, 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 Sep 21, 2026
  • easifish Public
    JaneliaSciComp/easifish's past year of commit activity
    Nextflow 2 BSD-3-Clause 1 2 0 Updated Sep 21, 2026
  • dis-utilities Public

    Utilities for Data and Information Services

    JaneliaSciComp/dis-utilities's past year of commit activity
    JavaScript 2 BSD-3-Clause 1 14 0 Updated Sep 21, 2026
  • cellpose-runner Public

    Repo for running cellpose with different configurations and saving timesamped directories

    JaneliaSciComp/cellpose-runner's past year of commit activity
    Python 0 BSD-3-Clause 0 0 1 Updated Sep 21, 2026
  • DatasetGateway Public

    Unified authorization service for datasets (Connectomics)

    JaneliaSciComp/DatasetGateway's past year of commit activity
    Python 0 0 0 0 Updated Sep 21, 2026
  • rnanix_server_frontend Public
    JaneliaSciComp/rnanix_server_frontend's past year of commit activity
    JavaScript 0 0 0 0 Updated Sep 19, 2026
  • neuronbridge Public

    EM/LM neuron search

    JaneliaSciComp/neuronbridge's past year of commit activity
    JavaScript 5 BSD-3-Clause 1 0 45 Updated Sep 19, 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 31 4 Updated Sep 18, 2026
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