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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.

Popular repositories Loading

  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 84 17

  3. RS-FISH RS-FISH Public

    Tool for precise, interactive, fast and scalable FISH spot detection

    Java 55 15

  4. multifish multifish Public

    EASI-FISH analysis pipeline for spatial transcriptomics

    Jupyter Notebook 36 13

  5. JRCLUST JRCLUST Public

    JRCLUST

    MATLAB 35 23

  6. multiview-reconstruction multiview-reconstruction Public

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

    Java 35 26

Repositories

Showing 10 of 356 repositories
  • jacs-cm Public

    JACS Configuration Management

    JaneliaSciComp/jacs-cm's past year of commit activity
    Shell 8 2 17 3 Updated Oct 9, 2026
  • embryo-harmonics Public

    Computing Laplace-eigenfunctions on geometrical models of C elegans embryos

    JaneliaSciComp/embryo-harmonics's past year of commit activity
    Python 0 BSD-3-Clause 0 0 0 Updated Oct 9, 2026
  • fileglancer Public

    Browse, share, and publish OME-Zarr data

    JaneliaSciComp/fileglancer's past year of commit activity
    TypeScript 30 BSD-3-Clause 5 1 17 Updated Oct 9, 2026
  • fileglancer-hub Public

    Production deployment scripts for Fileglancer

    JaneliaSciComp/fileglancer-hub's past year of commit activity
    0 BSD-3-Clause 0 0 0 Updated Oct 9, 2026
  • BigStitcher-Spark Public

    Running compute-intense parts of BigStitcher distributed

    JaneliaSciComp/BigStitcher-Spark's past year of commit activity
    Java 31 BSD-2-Clause 20 19 2 Updated Oct 9, 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 7 BSD-3-Clause 5 2 0 Updated Oct 9, 2026
  • dis-utilities Public

    Utilities for Data and Information Services

    JaneliaSciComp/dis-utilities's past year of commit activity
    Python 2 BSD-3-Clause 1 14 0 Updated Oct 9, 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 Oct 9, 2026
  • ecephys-pipeline Public
    JaneliaSciComp/ecephys-pipeline's past year of commit activity
    Python 0 0 0 0 Updated Oct 9, 2026
  • janelia-unity-toolkit Public

    Packages for the Unity game engine, emphasizing animal studies in VR.

    JaneliaSciComp/janelia-unity-toolkit's past year of commit activity
    C# 19 13 9 5 Updated Oct 9, 2026
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