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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 91 22

  2. BigStitcher BigStitcher Public

    ImgLib2/BDV implementation of Stitching for large datasets

    Java 78 17

  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 31 24

Repositories

Showing 10 of 303 repositories
  • easifish Public
    JaneliaSciComp/easifish’s past year of commit activity
    Nextflow 1 BSD-3-Clause 0 0 0 Updated Jan 16, 2026
  • fileglancer Public

    Browse, share, and publish OME-Zarr data

    JaneliaSciComp/fileglancer’s past year of commit activity
    TypeScript 17 BSD-3-Clause 2 0 6 Updated Jan 16, 2026
  • claude-howto Public
    JaneliaSciComp/claude-howto’s past year of commit activity
    Shell 1 0 0 0 Updated Jan 16, 2026
  • 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 Jan 16, 2026
  • SOFIMA-scripts Public

    wrapper to batch jobs to cluster

    JaneliaSciComp/SOFIMA-scripts’s past year of commit activity
    Python 1 BSD-3-Clause 1 0 0 Updated Jan 15, 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 5 Updated Jan 15, 2026
  • doi_common Public

    Library of common DOI-related functions for Python

    JaneliaSciComp/doi_common’s past year of commit activity
    Python 0 BSD-3-Clause 0 0 0 Updated Jan 15, 2026
  • G4_Display_Tools Public

    Collection of tools for the G4 LED arena displays.

    JaneliaSciComp/G4_Display_Tools’s past year of commit activity
    MATLAB 2 CC-BY-4.0 5 12 0 Updated Jan 15, 2026
  • jacs-dashboard Public

    Dashboard interface for the JACSv2 services ecosystem.

    JaneliaSciComp/jacs-dashboard’s past year of commit activity
    JavaScript 0 MIT 0 4 10 Updated Jan 15, 2026
  • containers Public

    Containers for workflow plugins

    JaneliaSciComp/containers’s past year of commit activity
    Python 0 BSD-3-Clause 0 0 1 Updated Jan 14, 2026
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