Skip to content
@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 354 repositories
  • rnanix_server_frontend Public
    JaneliaSciComp/rnanix_server_frontend's past year of commit activity
    JavaScript 0 1 0 1 Updated Oct 2, 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 0 0 Updated Oct 1, 2026
  • rna-cryoem-data-portal Public
    JaneliaSciComp/rna-cryoem-data-portal's past year of commit activity
    JavaScript 0 0 0 2 Updated Oct 1, 2026
  • 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 35 GPL-2.0 26 31 5 Updated Oct 1, 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 1, 2026
  • cellpose-runner Public

    Repo for running cellpose with different configurations and saving timesamped directories

    JaneliaSciComp/cellpose-runner's past year of commit activity
    Python 0 BSD-3-Clause 0 0 1 Updated Oct 1, 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 1, 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 1, 2026
  • webknossos-celegans Public Forked from scalableminds/webknossos

    Visualize, share and annotate your large 3D images online

    JaneliaSciComp/webknossos-celegans's past year of commit activity
    TypeScript 0 AGPL-3.0 44 0 0 Updated Sep 30, 2026
  • DatasetGateway Public

    Unified authorization service for datasets (Connectomics)

    JaneliaSciComp/DatasetGateway's past year of commit activity
    Python 0 0 0 0 Updated Oct 1, 2026
View all repositories