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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 80 17

  3. multifish multifish Public

    EASI-FISH analysis pipeline for spatial transcriptomics

    Jupyter Notebook 36 13

  4. JRCLUST JRCLUST Public

    JRCLUST

    MATLAB 35 22

  5. multiview-reconstruction multiview-reconstruction Public

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

    Java 33 25

  6. BigStitcher-Spark BigStitcher-Spark Public

    Running compute-intense parts of BigStitcher distributed

    Java 30 18

Repositories

Showing 10 of 318 repositories
  • tensorswitch Public

    This package provides a unified entry point and organized task modules for managing N5/Zarr dataset conversions and downsampling. It centralizes your workflow into a single pipeline to reduce manual work and errors.

    JaneliaSciComp/tensorswitch’s past year of commit activity
    Python 4 BSD-3-Clause 3 0 0 Updated Apr 22, 2026
  • easifish Public
    JaneliaSciComp/easifish’s past year of commit activity
    Nextflow 1 BSD-3-Clause 1 1 0 Updated Apr 22, 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 Apr 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 Apr 22, 2026
  • BigStitcher-Spark Public

    Running compute-intense parts of BigStitcher distributed

    JaneliaSciComp/BigStitcher-Spark’s past year of commit activity
    Java 30 BSD-2-Clause 18 19 2 Updated Apr 22, 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 33 GPL-2.0 25 30 6 Updated Apr 21, 2026
  • zarrcade Public

    Create web-based OME-Zarr galleries

    JaneliaSciComp/zarrcade’s past year of commit activity
    Python 23 BSD-3-Clause 0 1 0 Updated Apr 21, 2026
  • zarr-tools Public

    Zarr tools used by various nextflow modules

    JaneliaSciComp/zarr-tools’s past year of commit activity
    Python 0 BSD-3-Clause 0 0 0 Updated Apr 21, 2026
  • cyroet-ai Public
    JaneliaSciComp/cyroet-ai’s past year of commit activity
    Python 0 0 0 0 Updated Apr 21, 2026
  • ReiserFlyDiscoSettings Public

    Settings folder for Reiser Lab

    JaneliaSciComp/ReiserFlyDiscoSettings’s past year of commit activity
    Shell 0 0 0 0 Updated Apr 21, 2026
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