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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 93 22

  2. BigStitcher BigStitcher Public

    ImgLib2/BDV implementation of Stitching for large datasets

    Java 79 17

  3. JRCLUST JRCLUST Public

    JRCLUST

    MATLAB 35 22

  4. multifish multifish Public

    EASI-FISH analysis pipeline for spatial transcriptomics

    Jupyter Notebook 35 13

  5. multiview-reconstruction multiview-reconstruction Public

    Software for the reconstruction of multi-view microscopic acquisitions like Selective Plane Illumination Microscopy (SPIM) Data

    Java 32 24

  6. BigStitcher-Spark BigStitcher-Spark Public

    Running compute-intense parts of BigStitcher distributed

    Java 30 17

Repositories

Showing 10 of 312 repositories
  • bigstream Public

    Tools for distributed alignment of massive images

    JaneliaSciComp/bigstream’s past year of commit activity
    Jupyter Notebook 93 BSD-3-Clause 22 13 3 Updated Feb 24, 2026
  • easifish Public
    JaneliaSciComp/easifish’s past year of commit activity
    Nextflow 1 BSD-3-Clause 0 0 0 Updated Feb 24, 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 3 BSD-3-Clause 3 0 4 Updated Feb 24, 2026
  • fileglancer Public

    Browse, share, and publish OME-Zarr data

    JaneliaSciComp/fileglancer’s past year of commit activity
    TypeScript 19 BSD-3-Clause 2 0 8 Updated Feb 24, 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 32 GPL-2.0 24 30 7 Updated Feb 24, 2026
  • neuroglancer-mrc Public
    JaneliaSciComp/neuroglancer-mrc’s past year of commit activity
    Python 0 0 0 0 Updated Feb 24, 2026
  • py-cluster-api Public

    Python API for HPC clusters

    JaneliaSciComp/py-cluster-api’s past year of commit activity
    Python 0 BSD-3-Clause 0 0 0 Updated Feb 24, 2026
  • cellpose-tools Public

    Python code for the nf-cellpose pipeline

    JaneliaSciComp/cellpose-tools’s past year of commit activity
    Python 0 BSD-3-Clause 0 0 0 Updated Feb 24, 2026
  • fileglancer-demo-app Public
    JaneliaSciComp/fileglancer-demo-app’s past year of commit activity
    Python 0 BSD-3-Clause 0 0 0 Updated Feb 23, 2026
  • 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 Feb 23, 2026
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