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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 90 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 301 repositories
  • ReiserFlyDiscoSettings Public

    Settings folder for Reiser Lab

    JaneliaSciComp/ReiserFlyDiscoSettings’s past year of commit activity
    Shell 0 0 0 0 Updated Dec 21, 2025
  • 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 Dec 20, 2025
  • bigstream Public

    Tools for distributed alignment of massive images

    JaneliaSciComp/bigstream’s past year of commit activity
    Jupyter Notebook 90 BSD-3-Clause 22 13 3 Updated Dec 19, 2025
  • easifish Public
    JaneliaSciComp/easifish’s past year of commit activity
    Nextflow 1 BSD-3-Clause 0 0 0 Updated Dec 19, 2025
  • nextflow-modules Public

    Nextflow modules for use with nf-core tooling

    JaneliaSciComp/nextflow-modules’s past year of commit activity
    Nextflow 1 BSD-3-Clause 0 0 0 Updated Dec 19, 2025
  • nf-cellpose Public

    Nextflow pipeline for cellpose segmentation

    JaneliaSciComp/nf-cellpose’s past year of commit activity
    Nextflow 0 MIT 0 0 0 Updated Dec 19, 2025
  • 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 1 Updated Dec 19, 2025
  • fileglancer-hub Public

    Production deployment scripts for Fileglancer

    JaneliaSciComp/fileglancer-hub’s past year of commit activity
    0 BSD-3-Clause 0 0 0 Updated Dec 19, 2025
  • fileglancer Public

    Browse, share, and publish OME-Zarr data

    JaneliaSciComp/fileglancer’s past year of commit activity
    TypeScript 16 BSD-3-Clause 2 0 3 Updated Dec 19, 2025
  • Ax2 Public

    acoustic segmenter

    JaneliaSciComp/Ax2’s past year of commit activity
    Julia 0 BSD-3-Clause 0 0 0 Updated Dec 19, 2025
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