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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 86 21

  2. NIDAQ.jl NIDAQ.jl Public

    National Instruments Data Acquisition Interface

    Julia 49 16

  3. JRCLUST JRCLUST Public

    JRCLUST

    MATLAB 35 22

  4. multifish multifish Public

    EASI-FISH analysis pipeline for spatial transcriptomics

    Jupyter Notebook 35 13

  5. xarray-multiscale xarray-multiscale Public

    scalable multiscale image pyramids in python

    Python 29 3

  6. BigStitcher-Spark BigStitcher-Spark Public

    Running compute-intense parts of BigStitcher distributed

    Java 26 14

Repositories

Showing 10 of 287 repositories
  • SOFIMA-scripts Public

    wrapper to batch jobs to cluster

    JaneliaSciComp/SOFIMA-scripts’s past year of commit activity
    Python 0 0 0 0 Updated Sep 17, 2025
  • containers Public

    Containers for workflow plugins

    JaneliaSciComp/containers’s past year of commit activity
    Python 0 BSD-3-Clause 0 0 1 Updated Sep 16, 2025
  • 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 5 BSD-3-Clause 0 0 1 Updated Sep 16, 2025
  • fileglancer Public

    Browse, share, and publish data in the Janelia file system

    JaneliaSciComp/fileglancer’s past year of commit activity
    TypeScript 1 BSD-3-Clause 1 0 7 Updated Sep 16, 2025
  • EM_recon_pipeline Public

    Pipeline scripts and tools for reconstructing Electron Microscopy volumes.

    JaneliaSciComp/EM_recon_pipeline’s past year of commit activity
    Python 3 BSD-3-Clause 3 0 2 Updated Sep 16, 2025
  • easifish Public
    JaneliaSciComp/easifish’s past year of commit activity
    Nextflow 0 BSD-3-Clause 0 0 0 Updated Sep 16, 2025
  • bigstream Public

    Tools for distributed alignment of massive images

    JaneliaSciComp/bigstream’s past year of commit activity
    Jupyter Notebook 86 BSD-3-Clause 21 13 4 Updated Sep 16, 2025
  • jacs-compute Public

    JAnelia Compute Services (JACS)

    JaneliaSciComp/jacs-compute’s past year of commit activity
    Java 1 BSD-3-Clause 0 0 0 Updated Sep 16, 2025
  • x2s3 Public

    S3 Proxy Service

    JaneliaSciComp/x2s3’s past year of commit activity
    Python 9 BSD-3-Clause 0 0 0 Updated Sep 16, 2025
  • jacs-model Public

    JACS Domain Model and DAOs

    JaneliaSciComp/jacs-model’s past year of commit activity
    Java 1 BSD-3-Clause 0 0 1 Updated Sep 16, 2025
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