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@JaneliaSciComp Howard Hughes Medical Institute

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    Repositories list

    356 repositories

    • janelia-jhdf5

      Public
      SciJava JHDF5 from Janelia
      Java
      •
      Other
      •0•1•0•10•Updated Oct 6, 2026Oct 6, 2026

    • jacs-compute

      Public
      JAnelia Compute Services (JACS)
      distributed-computingneuroimagingcluster-computing
      distributed-computingneuroimagingcluster-computing
      Java
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•Updated Oct 6, 2026Oct 6, 2026

    • rnanix_server_frontend

      Public
      JavaScript
      •1•0•0•1•Updated Oct 5, 2026Oct 5, 2026

    • rna_atlas_website

      Public
      Python
      •0•0•0•0•Updated Oct 5, 2026Oct 5, 2026

    • jacs-model

      Public
      JACS Domain Model and DAOs
      Java
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•1•Updated Oct 5, 2026Oct 5, 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 i…
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •5•7•0•0•Updated Oct 5, 2026Oct 5, 2026

    • BigStitcher-Spark

      Public
      Running compute-intense parts of BigStitcher distributed
      Java
      •
      BSD 2-Clause "Simplified" License
      •20•31•19•2•Updated Oct 5, 2026Oct 5, 2026

    • dis-utilities

      Public
      Utilities for Data and Information Services
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•2•14•0•Updated Oct 5, 2026Oct 5, 2026

    • janelia-unity-toolkit

      Public
      Packages for the Unity game engine, emphasizing animal studies in VR.
      C#
      •
      Other
      •13•19•8•6•Updated Oct 5, 2026Oct 5, 2026

    • chunkmirage

      Public
      Serving virtual chunked files over https, suitable for neuroglancer browsing.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•Updated Oct 5, 2026Oct 5, 2026

    • rna-cryoem-data-portal

      Public
      Python
      •0•0•0•0•Updated Oct 5, 2026Oct 5, 2026

    • habitat_pipeline

      Public
      Integrated Multi-Animal Electrophysiology and Behavior Analysis Pipeline
      Jupyter Notebook
      •0•0•0•0•Updated Oct 5, 2026Oct 5, 2026

    • webknossos-celegans

      Public
      Visualize, share and annotate your large 3D images online
      TypeScript
      •
      GNU Affero General Public License v3.0
      •41•0•0•0•Updated Oct 5, 2026Oct 5, 2026

    • embryo-harmonics

      Public
      Computing Laplace-eigenfunctions on geometrical models of C elegans embryos
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Oct 5, 2026Oct 5, 2026

    • fileglancer-hub

      Public
      Production deployment scripts for Fileglancer
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Oct 5, 2026Oct 5, 2026

    • fileglancer

      Public
      Browse, share, and publish OME-Zarr data
      microscopyimagingzarr
      microscopyimagingzarrngffome-zarrome-ngff
      TypeScript
      •
      BSD 3-Clause "New" or "Revised" License
      •5•30•1•14•Updated Oct 5, 2026Oct 5, 2026

    • multiview-reconstruction

      Public
      Software for the reconstruction of multi-view microscopic acquisitions like Selective Plane Illumination Microscopy (SPIM) Data
      Java
      •
      GNU General Public License v2.0
      •26•35•33•5•Updated Oct 5, 2026Oct 5, 2026

    • neuronbridge

      Public
      EM/LM neuron search
      awsneuroscienceneuroimaging
      awsneuroscienceneuroimagingneuronsdrosophilajanelia
      JavaScript
      •
      BSD 3-Clause "New" or "Revised" License
      •1•5•0•45•Updated Oct 3, 2026Oct 3, 2026

    • EM_recon_pipeline

      Public
      Pipeline scripts and tools for reconstructing Electron Microscopy volumes.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•5•0•8•Updated Oct 2, 2026Oct 2, 2026

    • cellpose-runner

      Public
      Repo for running cellpose with different configurations and saving timesamped directories
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•1•Updated Oct 1, 2026Oct 1, 2026

    • DatasetGateway

      Public
      Unified authorization service for datasets (Connectomics)
      Python
      •0•0•0•0•Updated Oct 1, 2026Oct 1, 2026

    • neuroglancer

      Public
      WebGL-based viewer for volumetric data
      TypeScript
      •
      Apache License 2.0
      •400•0•0•0•Updated Sep 30, 2026Sep 30, 2026

    • fibsem-pipeline-digest

      Public
      Small AI tool to summarize the current state of the fibsem pipeline for biweekly meetings.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Sep 30, 2026Sep 30, 2026

    • h5j-ng-viewer

      Public
      Browser-only H5J to OME-Zarr to Neuroglancer viewer. No backend, no upload.
      TypeScript
      •0•0•0•0•Updated Sep 29, 2026Sep 29, 2026

    • diff-rsync-o

      Public
      Linux scripts for transferring data from rig computers
      Shell
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•Updated Sep 29, 2026Sep 29, 2026

    • mrc-ng-server

      Public
      Serve MRC tomograms to Neuroglancer via the precomputed protocol
      Python
      •0•0•0•0•Updated Sep 28, 2026Sep 28, 2026

    • doi_common

      Public
      Library of common DOI-related functions for Python
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Sep 25, 2026Sep 25, 2026

    • VVDViewer

      Public
      3D/4D volumetric rendering of microscopy data
      renderingneurosciencemicroscopy
      renderingneurosciencemicroscopyvvd-viewer
      C++
      •
      BSD 3-Clause "New" or "Revised" License
      •7•28•4•4•Updated Sep 25, 2026Sep 25, 2026

    • flythrough

      Public
      Facilitates the creation of flythough microscopy volume videos via BigDataViewer
      Java
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Sep 24, 2026Sep 24, 2026

    • triton-sam2

      Public
      SAM2 deployed with Triton Inference Server
      Python
      •1•4•0•0•Updated Sep 24, 2026Sep 24, 2026
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