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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 359 repositories
  • janelia-pathlib Public

    Python library for auto-translating file share paths between operating systems.

    JaneliaSciComp/janelia-pathlib's past year of commit activity
    Python 3 BSD-3-Clause 0 0 2 Updated Oct 18, 2026
  • dataset-registry Public

    Metadata and structured, versioned notes about datasets and their relationships

    JaneliaSciComp/dataset-registry's past year of commit activity
    Python 0 BSD-3-Clause 0 1 0 Updated Oct 18, 2026
  • janelia-jhdf5 Public

    SciJava JHDF5 from Janelia

    JaneliaSciComp/janelia-jhdf5's past year of commit activity
    Java 1 1 0 3 Updated Oct 16, 2026
  • VVDViewer Public

    3D/4D volumetric rendering of microscopy data

    JaneliaSciComp/VVDViewer's past year of commit activity
    C++ 28 BSD-3-Clause 6 4 5 Updated Oct 16, 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 16, 2026
  • mia-workflow-prototype Public
    JaneliaSciComp/mia-workflow-prototype's past year of commit activity
    Python 0 0 6 0 Updated Oct 16, 2026
  • chunkmirage Public

    Serve virtual chunked arrays (Zarr, N5, precomputed) over HTTP: each chunk computed on request by a pipeline you can edit live.

    JaneliaSciComp/chunkmirage's past year of commit activity
    Python 2 BSD-3-Clause 0 0 0 Updated Oct 16, 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 16, 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 8 3 Updated Oct 16, 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 1 Updated Oct 16, 2026
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