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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 93 23

  2. BigStitcher BigStitcher Public

    ImgLib2/BDV implementation of Stitching for large datasets

    Java 80 17

  3. JRCLUST JRCLUST Public

    JRCLUST

    MATLAB 35 22

  4. multifish multifish Public

    EASI-FISH analysis pipeline for spatial transcriptomics

    Jupyter Notebook 35 13

  5. multiview-reconstruction multiview-reconstruction Public

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

    Java 32 24

  6. BigStitcher-Spark BigStitcher-Spark Public

    Running compute-intense parts of BigStitcher distributed

    Java 30 17

Repositories

Showing 10 of 312 repositories
  • fileglancer Public

    Browse, share, and publish OME-Zarr data

    JaneliaSciComp/fileglancer’s past year of commit activity
    TypeScript 19 BSD-3-Clause 3 1 7 Updated Mar 4, 2026
  • nextflow-modules Public

    Nextflow modules for use with nf-core tooling

    JaneliaSciComp/nextflow-modules’s past year of commit activity
    Nextflow 1 BSD-3-Clause 0 0 0 Updated Mar 4, 2026
  • dis-utilities Public

    Utilities for Data and Information Services

    JaneliaSciComp/dis-utilities’s past year of commit activity
    JavaScript 2 BSD-3-Clause 1 14 1 Updated Mar 4, 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 Mar 4, 2026
  • BigStitcher-Spark Public

    Running compute-intense parts of BigStitcher distributed

    JaneliaSciComp/BigStitcher-Spark’s past year of commit activity
    Java 30 BSD-2-Clause 17 19 2 Updated Mar 4, 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 32 GPL-2.0 24 30 7 Updated Mar 4, 2026
  • easifish Public
    JaneliaSciComp/easifish’s past year of commit activity
    Nextflow 1 BSD-3-Clause 0 0 0 Updated Mar 4, 2026
  • fileglancer-hub Public

    Production deployment scripts for Fileglancer

    JaneliaSciComp/fileglancer-hub’s past year of commit activity
    0 BSD-3-Clause 0 0 2 Updated Mar 4, 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 Mar 4, 2026
  • cellpose-tools Public

    Python code for the nf-cellpose pipeline

    JaneliaSciComp/cellpose-tools’s past year of commit activity
    Python 0 BSD-3-Clause 0 0 0 Updated Mar 3, 2026
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