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    339 repositories

    • Brain-aligner-CDM-cleater-pipeline

      Public
      Java
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Aug 20, 2026Aug 20, 2026

    • dis-utilities

      Public
      Utilities for Data and Information Services
      JavaScript
      •
      BSD 3-Clause "New" or "Revised" License
      •1•2•14•0•Updated Aug 20, 2026Aug 20, 2026

    • x2s3

      Public
      S3 Proxy Service
      s3s3-buckets3-storage
      s3s3-buckets3-storage
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•13•1•1•Updated Aug 20, 2026Aug 20, 2026

    • spotlight

      Public
      This repository handles shading and intensity correction for large microscopy image datasets.
      Python
      •0•0•0•0•Updated Aug 20, 2026Aug 20, 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•9•Updated Aug 20, 2026Aug 20, 2026

    • spearmint

      Public
      Runs DB + dag-based task runner. LSF or local. "A tool for organizing your exspearmints."
      Python
      •0•0•0•0•Updated Aug 19, 2026Aug 19, 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•2•Updated Aug 19, 2026Aug 19, 2026

    • DatasetGateway

      Public
      Unified authorization service for datasets (Connectomics)
      Python
      •0•0•0•0•Updated Aug 19, 2026Aug 19, 2026

    • jacs-storage

      Public
      JADE file storage services
      Java
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•1•Updated Aug 19, 2026Aug 19, 2026

    • neuroglancer

      Public
      WebGL-based viewer for volumetric data
      TypeScript
      •
      Apache License 2.0
      •378•0•0•0•Updated Aug 19, 2026Aug 19, 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
      •4•8•0•0•Updated Aug 19, 2026Aug 19, 2026

    • fileglancer

      Public
      Browse, share, and publish OME-Zarr data
      microscopyimagingzarr
      microscopyimagingzarrngffome-zarrome-ngff
      TypeScript
      •
      BSD 3-Clause "New" or "Revised" License
      •5•29•1•11•Updated Aug 19, 2026Aug 19, 2026

    • easifish

      Public
      Nextflow
      •
      BSD 3-Clause "New" or "Revised" License
      •1•2•2•0•Updated Aug 19, 2026Aug 19, 2026

    • CommonExpressionLanguage.jl

      Public
      Julia
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•Updated Aug 18, 2026Aug 18, 2026

    • neuroglancer-mrc

      Public
      Python
      •1•1•0•0•Updated Aug 18, 2026Aug 18, 2026

    • bigstream

      Public
      Tools for distributed alignment of massive images
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •25•95•13•3•Updated Aug 17, 2026Aug 17, 2026

    • ThreeD_Neuron_Segmentation

      Public
      LM confocal data, 3D neuron segmentation
      Java
      •
      MIT License
      •0•0•0•0•Updated Aug 17, 2026Aug 17, 2026

    • Skeleton_Creation_Branch_Analysis

      Public
      Fiji/ImageJ macro and plugin workflow for skeleton branch analysis of 40x brain neuron volumes.
      Java
      •0•0•0•0•Updated Aug 17, 2026Aug 17, 2026

    • jacs-cm

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

    • mrc-ng-server

      Public
      Serve MRC tomograms to Neuroglancer via the precomputed protocol
      Python
      •0•0•0•1•Updated Aug 16, 2026Aug 16, 2026

    • rna_atlas_website

      Public
      Python
      •0•0•0•0•Updated Aug 16, 2026Aug 16, 2026

    • fileglancer-janelia

      Public
      Janelia-specific scripts for Fileglancer
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Aug 14, 2026Aug 14, 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•34•30•6•Updated Aug 12, 2026Aug 12, 2026

    • BigStitcher-Spark

      Public
      Running compute-intense parts of BigStitcher distributed
      Java
      •
      BSD 2-Clause "Simplified" License
      •20•31•19•2•Updated Aug 11, 2026Aug 11, 2026

    • janelia-pycookie

      Public archive
      A cookiecutter for creating a new Python library
      Python
      •0•0•0•0•Updated Aug 11, 2026Aug 11, 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•50•0•Updated Aug 11, 2026Aug 11, 2026

    • neuronbridge

      Public
      EM/LM neuron search
      awsneuroscienceneuroimaging
      awsneuroscienceneuroimagingneuronsdrosophilajanelia
      JavaScript
      •
      BSD 3-Clause "New" or "Revised" License
      •1•5•0•41•Updated Aug 10, 2026Aug 10, 2026

    • workstation

      Public
      Janelia Workstation
      neurosciencescientific-computingneuroimaging
      neurosciencescientific-computingneuroimagingvolume-renderingconnectomicsjaneliaconfocal-microscopy
      Java
      •
      Other
      •12•29•1•7•Updated Aug 10, 2026Aug 10, 2026

    • warp-atlas-viewer

      Public
      Interactive web-based atlas for the WARP dataset
      TypeScript
      •0•0•0•0•Updated Aug 10, 2026Aug 10, 2026

    • easifish-spots-tools

      Public
      Various tools used by EASI-FISH pipeline for processing spots
      Python
      •0•0•0•0•Updated Aug 10, 2026Aug 10, 2026
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