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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. 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 25

  6. BigStitcher-Spark BigStitcher-Spark Public

    Running compute-intense parts of BigStitcher distributed

    Java 30 18

Repositories

Showing 10 of 317 repositories
  • ShroffCelegansModels.jl Public
    JaneliaSciComp/ShroffCelegansModels.jl’s past year of commit activity
    Julia 3 MIT 1 0 43 Updated Apr 18, 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 4 BSD-3-Clause 3 8 0 Updated Apr 17, 2026
  • neuronbridge Public

    EM/LM neuron search

    JaneliaSciComp/neuronbridge’s past year of commit activity
    JavaScript 5 BSD-3-Clause 1 0 17 Updated Apr 17, 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 17, 2026
  • DatasetGateway Public

    Unified authorization service for datasets (Connectomics)

    JaneliaSciComp/DatasetGateway’s past year of commit activity
    Python 0 0 0 0 Updated Apr 17, 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 16, 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 Apr 16, 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 Apr 16, 2026
  • fileglancer Public

    Browse, share, and publish OME-Zarr data

    JaneliaSciComp/fileglancer’s past year of commit activity
    TypeScript 25 BSD-3-Clause 4 1 5 Updated Apr 16, 2026
  • easifish Public
    JaneliaSciComp/easifish’s past year of commit activity
    Nextflow 1 BSD-3-Clause 1 0 0 Updated Apr 16, 2026
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