Repositories list

• EM_recon_pipeline

  Public
  Pipeline scripts and tools for reconstructing Electron Microscopy volumes.

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •3•3•0•3•Updated Mar 16, 2025Mar 16, 2025

• BigStitcher-Spark

  Public
  Running compute-intense parts of BigStitcher distributed

  Java

  •

  BSD 2-Clause "Simplified" License

  •13•24•15•0•Updated Mar 15, 2025Mar 15, 2025

• fileglancer

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

  CSS

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated Mar 14, 2025Mar 14, 2025

• neuronbridge-precompute

  Public
  Utilities for indexing and transferring of NeuronBridge-related files

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated Mar 14, 2025Mar 14, 2025

• jacs-cm

  Public
  JACS Configuration Management

  janeliajanelia-workstationmouselight+ 4dockerdevopsdocker-swarmswarm

  XSLT

  •

  Other

  •3•8•17•3•Updated Mar 14, 2025Mar 14, 2025

• dis-utilities

  Public
  Utilities for Data and Information Services

  JavaScript

  •

  BSD 3-Clause "New" or "Revised" License

  •1•1•14•1•Updated Mar 14, 2025Mar 14, 2025

• transfero-linux

  Public
  Linux scripts for transferring data from rig computers

  Shell

  •

  BSD 3-Clause "New" or "Revised" License

  •0•1•1•0•Updated Mar 13, 2025Mar 13, 2025

• jacs-storage

  Public
  JADE file storage services

  Java

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•1•Updated Mar 13, 2025Mar 13, 2025

• hortacloud-website

  Public
  Documentation website for HortaCloud

  neurosciencejaneliahortacloud

  HTML

  •

  BSD 3-Clause "New" or "Revised" License

  •0•2•0•4•Updated Mar 12, 2025Mar 12, 2025

• transfero

  Public
  Python scripts for transferring data from rig computers

  Python

  •0•0•2•0•Updated Mar 12, 2025Mar 12, 2025

• neuronbridge

  Public
  EM/LM neuron search

  neuroscienceneuroimagingneurons+ 3drosophilajaneliaaws

  JavaScript

  •

  BSD 3-Clause "New" or "Revised" License

  •1•4•0•11•Updated Mar 12, 2025Mar 12, 2025

• G4_Display_Tools

  Public
  Collection of tools for the G4 LED arena displays.

  MATLAB

  •

  Creative Commons Attribution 4.0 International

  •4•2•12•0•Updated Mar 11, 2025Mar 11, 2025

• fileglancer-central

  Public
  Central metadata server for Fileglancer deployments

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•1•Updated Mar 11, 2025Mar 11, 2025

• ossi-website

  Public
  Website showcasing Janelia Open Science Software Intiative (OSSI) supported software projects and other software developed at Janelia.

  Astro

  •

  BSD 3-Clause "New" or "Revised" License

  •18•1•16•2•Updated Mar 10, 2025Mar 10, 2025

• dvid-point-cloud

  Public
  Library for creating point clouds for sparse volumes within DVID

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •1•1•0•0•Updated Mar 10, 2025Mar 10, 2025

• hortacloud

  Public
  HortaCloud - 3D annotation platform for large microscopy data

  awsneurosciencescientific-computing+ 3neuronsannotation-tooljanelia

  JavaScript

  •

  BSD 3-Clause "New" or "Revised" License

  •1•10•47•0•Updated Mar 10, 2025Mar 10, 2025

• workstation

  Public
  Janelia Workstation

  neurosciencescientific-computingneuroimaging+ 4volume-renderingconnectomicsjaneliaconfocal-microscopy

  Java

  •

  Other

  •11•23•0•13•Updated Mar 10, 2025Mar 10, 2025

• pydantic-ome-ngff

  Public
  Pydantic models for OME-NGFF

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •3•23•6•1•Updated Mar 10, 2025Mar 10, 2025

• x2s3

  Public
  S3 Proxy Service

  s3s3-buckets3-storage

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •0•7•0•1•Updated Mar 10, 2025Mar 10, 2025

• easifish

  Public
  Nextflow

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated Mar 8, 2025Mar 8, 2025

• nextflow-modules

  Public
  Nextflow modules for use with nf-core tooling

  Nextflow

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated Mar 8, 2025Mar 8, 2025

• colormipsearch

  Public
  Distributed Color Depth MIP Search

  neurosciencesearch-algorithmneuron

  Java

  •

  BSD 3-Clause "New" or "Revised" License

  •1•1•0•2•Updated Mar 7, 2025Mar 7, 2025

• doi_common

  Public
  Library of common DOI-related functions for Python

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated Mar 7, 2025Mar 7, 2025

• videoAnnotation

  Public
  JavaScript

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated Mar 6, 2025Mar 6, 2025

• containers

  Public
  Containers for workflow plugins

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated Mar 5, 2025Mar 5, 2025

• jacs-compute

  Public
  JAnelia Compute Services (JACS)

  distributed-computingneuroimagingcluster-computing

  Java

  •

  BSD 3-Clause "New" or "Revised" License

  •0•1•0•0•Updated Mar 4, 2025Mar 4, 2025

• jacs-model

  Public
  JACS Domain Model and DAOs

  Java

  •

  BSD 3-Clause "New" or "Revised" License

  •0•1•0•0•Updated Mar 4, 2025Mar 4, 2025

• EM_MIP_search

  Public
  Java

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated Mar 3, 2025Mar 3, 2025

• Zarr.jl

  Public
  Janelia fork of Zarr.jl

  Julia

  •

  Other

  •27•0•0•0•Updated Mar 2, 2025Mar 2, 2025

• janelia-unity-toolkit

  Public
  Packages for the Unity game engine, emphasizing animal studies in VR.

  C#

  •

  Other

  •11•16•5•2•Updated Mar 1, 2025Mar 1, 2025