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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 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 358 repositories
  • 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 15, 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 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 5 BSD-3-Clause 3 0 8 Updated Oct 14, 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 14, 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 4 Updated Oct 14, 2026
  • spotlight Public

    This repository handles shading and intensity correction for large microscopy image datasets.

    JaneliaSciComp/spotlight's past year of commit activity
    Python 2 0 0 0 Updated Oct 14, 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 4 Updated Oct 14, 2026
  • rna_atlas_website Public
    JaneliaSciComp/rna_atlas_website's past year of commit activity
    Python 1 0 0 0 Updated Oct 14, 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 14, 2026
  • rna-cryoem-data-portal Public
    JaneliaSciComp/rna-cryoem-data-portal's past year of commit activity
    Python 0 0 0 0 Updated Oct 14, 2026
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