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    317 repositories

    • easifish

      Public
      Nextflow
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•0•0•Updated Apr 10, 2026Apr 10, 2026

    • fileglancer

      Public
      Browse, share, and publish OME-Zarr data
      microscopyimagingzarr
      microscopyimagingzarrngffome-zarrome-ngff
      TypeScript
      •
      BSD 3-Clause "New" or "Revised" License
      •4•22•0•3•Updated Apr 10, 2026Apr 10, 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
      •24•33•30•6•Updated Apr 10, 2026Apr 10, 2026

    • DatasetGateway

      Public
      Unified authorization service for datasets (Connectomics)
      Python
      •0•0•0•0•Updated Apr 10, 2026Apr 10, 2026

    • SongExplorer

      Public
      deep learning for acoustic signals
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •6•24•5•1•Updated Apr 10, 2026Apr 10, 2026

    • ephys-pipeline

      Public
      Pipeline to process electrophysiology data.
      Python
      •0•0•6•0•Updated Apr 10, 2026Apr 10, 2026

    • es-responder

      Public
      Lightweight custom REST API for ElasticSearch queries
      JavaScript
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Apr 10, 2026Apr 10, 2026

    • EM_recon_pipeline

      Public
      Pipeline scripts and tools for reconstructing Electron Microscopy volumes.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•4•0•8•Updated Apr 10, 2026Apr 10, 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
      •3•4•8•0•Updated Apr 9, 2026Apr 9, 2026

    • ai-assisted-dev

      Public
      Presentation and resources on AI-assisted software development practices
      0•3•0•0•Updated Apr 9, 2026Apr 9, 2026

    • dis-utilities

      Public
      Utilities for Data and Information Services
      JavaScript
      •
      BSD 3-Clause "New" or "Revised" License
      •1•2•14•1•Updated Apr 9, 2026Apr 9, 2026

    • neuronbridge-vol-viewer

      Public
      Website incorporating @janelia/web-vol-viewer for direct volume rendering of neuronbridge matches
      JavaScript
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Apr 9, 2026Apr 9, 2026

    • janelia-unity-toolkit

      Public
      Packages for the Unity game engine, emphasizing animal studies in VR.
      C#
      •
      Other
      •13•18•7•3•Updated Apr 8, 2026Apr 8, 2026

    • BigStitcher-Spark

      Public
      Running compute-intense parts of BigStitcher distributed
      Java
      •
      BSD 2-Clause "Simplified" License
      •17•30•19•2•Updated Apr 8, 2026Apr 8, 2026

    • workstation-website

      Public
      Brochure website for the Janelia Workstation
      HTML
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•1•Updated Apr 8, 2026Apr 8, 2026

    • nextflow-modules

      Public
      Nextflow modules for use with nf-core tooling
      Nextflow
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•Updated Apr 7, 2026Apr 7, 2026

    • hortacloud

      Public
      HortaCloud - 3D annotation platform for large microscopy data
      awsneurosciencescientific-computing
      awsneurosciencescientific-computingneuronsannotation-tooljanelia
      JavaScript
      •
      BSD 3-Clause "New" or "Revised" License
      •1•10•49•0•Updated Apr 7, 2026Apr 7, 2026

    • triton-sam2

      Public
      SAM2 deployed with Triton Inference Server
      Python
      •0•3•0•0•Updated Apr 7, 2026Apr 7, 2026

    • PEELing_web

      Public
      JavaScript
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Apr 6, 2026Apr 6, 2026

    • containers

      Public
      Containers for workflow plugins
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•1•Updated Apr 6, 2026Apr 6, 2026

    • SOFIMA-scripts

      Public
      wrapper to batch jobs to cluster
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•0•0•Updated Apr 3, 2026Apr 3, 2026

    • jrc-rna-structure-pipeline

      Public
      Workflow to extract, process, and curate RNA 3D structural data from PDB for structure prediction tasks
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•5•1•0•Updated Apr 3, 2026Apr 3, 2026

    • cellpose-tools

      Public
      Python code for the nf-cellpose pipeline
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Apr 2, 2026Apr 2, 2026

    • neuronbridge

      Public
      EM/LM neuron search
      awsneuroscienceneuroimaging
      awsneuroscienceneuroimagingneuronsdrosophilajanelia
      JavaScript
      •
      BSD 3-Clause "New" or "Revised" License
      •1•5•0•17•Updated Apr 1, 2026Apr 1, 2026

    • easifish-spots-tools

      Public
      Various tools used by EASI-FISH pipeline for processing spots
      Python
      •0•0•0•0•Updated Apr 1, 2026Apr 1, 2026

    • jacs-cm

      Public
      JACS Configuration Management
      dockerdevopsdocker-swarm
      dockerdevopsdocker-swarmswarmjaneliajanelia-workstationmouselight
      Shell
      •
      Other
      •2•8•17•3•Updated Mar 31, 2026Mar 31, 2026

    • bigstream

      Public
      Tools for distributed alignment of massive images
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •25•95•13•3•Updated Mar 31, 2026Mar 31, 2026

    • neuronbridge-services

      Public
      AWS Services for NeuronBridge
      JavaScript
      •
      BSD 3-Clause "New" or "Revised" License
      •2•2•0•19•Updated Mar 31, 2026Mar 31, 2026

    • napari-worm

      Public
      3D Cell Annotation Tool for C. elegans using Napari
      Python
      •0•0•0•0•Updated Mar 30, 2026Mar 30, 2026

    • videoAnnotation

      Public
      JavaScript
      •
      BSD 3-Clause "New" or "Revised" License
      •0•2•0•0•Updated Mar 30, 2026Mar 30, 2026
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