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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 89 21

  2. BigStitcher BigStitcher Public

    ImgLib2/BDV implementation of Stitching for large datasets

    Java 77 16

  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 29 24

Repositories

Showing 10 of 295 repositories
  • 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 Nov 17, 2025
  • neuronbridge Public

    EM/LM neuron search

    JaneliaSciComp/neuronbridge’s past year of commit activity
    JavaScript 5 BSD-3-Clause 1 0 12 Updated Nov 17, 2025
  • 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 29 GPL-2.0 24 28 6 Updated Nov 17, 2025
  • fileglancer Public

    Browse, share, and publish OME-Zarr data

    JaneliaSciComp/fileglancer’s past year of commit activity
    TypeScript 15 BSD-3-Clause 2 0 2 Updated Nov 17, 2025
  • 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 Nov 14, 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 Nov 14, 2025
  • neuronbridge-precompute Public

    Utilities for indexing and transferring of NeuronBridge-related files

    JaneliaSciComp/neuronbridge-precompute’s past year of commit activity
    Python 0 BSD-3-Clause 0 0 0 Updated Nov 14, 2025
  • micropattern_cell_analysis Public

    Micropattern Cell Analysis for the Gladkova and Vale Labs

    JaneliaSciComp/micropattern_cell_analysis’s past year of commit activity
    Python 0 BSD-3-Clause 0 0 0 Updated Nov 14, 2025
  • flycore-utilities Public

    Utility programs for synchronization with the Fly Facility's FLYF2 database

    JaneliaSciComp/flycore-utilities’s past year of commit activity
    Python 1 BSD-3-Clause 0 0 0 Updated Nov 14, 2025
  • easifish Public
    JaneliaSciComp/easifish’s past year of commit activity
    Nextflow 1 BSD-3-Clause 0 0 0 Updated Nov 14, 2025
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