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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 83 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 34 26

Repositories

Showing 10 of 350 repositories
  • ShroffCelegansModels.jl Public
    JaneliaSciComp/ShroffCelegansModels.jl's past year of commit activity
    Julia 3 MIT 1 0 48 Updated Sep 14, 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 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
    Astro 1 BSD-3-Clause 21 16 2 Updated Sep 14, 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 4 BSD-3-Clause 3 0 8 Updated Sep 14, 2026
  • containers Public

    Containers for workflow plugins

    JaneliaSciComp/containers's past year of commit activity
    Python 0 BSD-3-Clause 0 0 1 Updated Sep 14, 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 12, 2026
  • neuroglancer Public Forked from google/neuroglancer

    WebGL-based viewer for volumetric data

    JaneliaSciComp/neuroglancer's past year of commit activity
    TypeScript 0 Apache-2.0 405 0 0 Updated Sep 12, 2026
  • n5-ng-precomputed Public

    Neuroglancer-precomputed backend for N5

    JaneliaSciComp/n5-ng-precomputed's past year of commit activity
    Java 0 BSD-3-Clause 1 0 0 Updated Sep 11, 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 11, 2026
  • habitat_pipeline Public

    Integrated Multi-Animal Electrophysiology and Behavior Analysis Pipeline

    JaneliaSciComp/habitat_pipeline's past year of commit activity
    Jupyter Notebook 0 0 0 0 Updated Sep 11, 2026
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