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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 94 24

  2. BigStitcher BigStitcher Public

    ImgLib2/BDV implementation of Stitching for large datasets

    Java 80 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 33 24

  6. BigStitcher-Spark BigStitcher-Spark Public

    Running compute-intense parts of BigStitcher distributed

    Java 30 17

Repositories

Showing 10 of 315 repositories
  • fileglancer Public

    Browse, share, and publish OME-Zarr data

    JaneliaSciComp/fileglancer’s past year of commit activity
    TypeScript 20 BSD-3-Clause 4 0 10 Updated Mar 26, 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 24 30 6 Updated Mar 26, 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 1 Updated Mar 26, 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 20 16 3 Updated Mar 25, 2026
  • easifish Public
    JaneliaSciComp/easifish’s past year of commit activity
    Nextflow 1 BSD-3-Clause 0 0 0 Updated Mar 25, 2026
  • easifish-spots-tools Public

    Various tools used by EASI-FISH pipeline for processing spots

    JaneliaSciComp/easifish-spots-tools’s past year of commit activity
    Python 0 0 0 0 Updated Mar 25, 2026
  • 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 3 BSD-3-Clause 3 8 0 Updated Mar 25, 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 Mar 25, 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 Mar 25, 2026
  • bigstream Public

    Tools for distributed alignment of massive images

    JaneliaSciComp/bigstream’s past year of commit activity
    Jupyter Notebook 94 BSD-3-Clause 24 13 3 Updated Mar 25, 2026
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