Repositories list

• dis-utilities

  Public
  Utilities for Data and Information Services

  JavaScript

  •

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

  •1•1•13•1•Updated Feb 21, 2025Feb 21, 2025

• EM_recon_pipeline

  Public
  Pipeline scripts and tools for reconstructing Electron Microscopy volumes.

  Python

  •

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

  •3•3•0•7•Updated Feb 20, 2025Feb 20, 2025

• fileglancer

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

  Python

  •

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

  •0•0•2•0•Updated Feb 20, 2025Feb 20, 2025

• jacs-tools-docker

  Public
  Tools for JACS, containerized with Docker

  ImageJ Macro

  •

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

  •0•0•0•0•Updated Feb 20, 2025Feb 20, 2025

• FunkeAnnotation

  Public
  Small tool to annotate images

  Java

  •0•0•0•0•Updated Feb 20, 2025Feb 20, 2025

• neuronbridge-services

  Public
  AWS Services for NeuronBridge

  JavaScript

  •

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

  •1•2•0•19•Updated Feb 20, 2025Feb 20, 2025

• BigStitcher-Spark

  Public
  Running compute-intense parts of BigStitcher distributed

  Java

  •

  BSD 2-Clause "Simplified" License

  •12•23•15•0•Updated Feb 20, 2025Feb 20, 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 Feb 20, 2025Feb 20, 2025

• containers

  Public
  Containers for workflow plugins

  Python

  •

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

  •0•0•0•0•Updated Feb 20, 2025Feb 20, 2025

• jacs-compute

  Public
  JAnelia Compute Services (JACS)

  distributed-computingneuroimagingcluster-computing

  Java

  •

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

  •0•1•0•0•Updated Feb 19, 2025Feb 19, 2025

• hortacloud-website

  Public
  Documentation website for HortaCloud

  neurosciencejaneliahortacloud

  HTML

  •

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

  •0•2•0•2•Updated Feb 19, 2025Feb 19, 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•17•3•Updated Feb 19, 2025Feb 19, 2025

• workday-utilities

  Public
  Utilities for getting data from Workday

  Python

  •

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

  •0•1•0•0•Updated Feb 18, 2025Feb 18, 2025

• storage-utilities

  Public
  Utilities for storage monitoring

  Python

  •

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

  •0•0•0•0•Updated Feb 18, 2025Feb 18, 2025

• aitch

  Public
  local scheduler for heterogenous jobs

  Rust

  •

  Other

  •0•3•0•0•Updated Feb 18, 2025Feb 18, 2025

• workstation

  Public
  Janelia Workstation

  neurosciencescientific-computingneuroimaging+ 4volume-renderingconnectomicsjaneliaconfocal-microscopy

  Java

  •

  Other

  •11•23•0•13•Updated Feb 18, 2025Feb 18, 2025

• VVDViewer

  Public
  3D/4D volumetric rendering of microscopy data

  renderingneurosciencemicroscopy+ 1vvd-viewer

  C++

  •

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

  •5•21•3•1•Updated Feb 14, 2025Feb 14, 2025

• janelia-unity-toolkit

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

  C#

  •

  Other

  •11•16•5•2•Updated Feb 13, 2025Feb 13, 2025

• bigstream

  Public
  Tools for distributed alignment of massive images

  Jupyter Notebook

  •

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

  •21•80•12•1•Updated Feb 13, 2025Feb 13, 2025

• easifish

  Public
  Nextflow

  •

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

  •0•0•0•0•Updated Feb 13, 2025Feb 13, 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 Feb 13, 2025Feb 13, 2025

• jacs-cm

  Public
  JACS Configuration Management

  janeliajanelia-workstationmouselight+ 4dockerdevopsdocker-swarmswarm

  XSLT

  •

  Other

  •3•8•17•3•Updated Feb 13, 2025Feb 13, 2025

• SongExplorer

  Public
  deep learning for acoustic signals

  Python

  •

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

  •6•24•5•1•Updated Feb 13, 2025Feb 13, 2025

• jrc_common

  Public
  Library of common utility functions for Python

  Python

  •

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

  •0•0•0•0•Updated Feb 11, 2025Feb 11, 2025

• pydantic-ome-ngff

  Public
  Pydantic models for OME-NGFF

  Python

  •

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

  •3•22•6•1•Updated Feb 10, 2025Feb 10, 2025

• bossdb-convert

  Public
  Downloads and converts bossdb.org data using intern and tensorstore

  Jupyter Notebook

  •0•0•0•0•Updated Feb 10, 2025Feb 10, 2025

• ShroffCelegansModels.jl

  Public
  Julia

  •

  MIT License

  •0•2•0•40•Updated Feb 7, 2025Feb 7, 2025

• neuronbridge

  Public
  EM/LM neuron search

  neuroscienceneuroimagingneurons+ 3drosophilajaneliaaws

  JavaScript

  •

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

  •1•4•0•10•Updated Feb 6, 2025Feb 6, 2025

• G4_Display_Tools

  Public
  Collection of tools for the G4 LED arena displays.

  MATLAB

  •

  Creative Commons Attribution 4.0 International

  •4•2•11•0•Updated Feb 6, 2025Feb 6, 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 Feb 5, 2025Feb 5, 2025