Repositories list

• janelia-unity-toolkit

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

  C#

  •

  Other

  •11•17•6•3•Updated Aug 13, 2025Aug 13, 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•46•0•Updated Aug 13, 2025Aug 13, 2025

• BigStitcher-Spark

  Public
  Running compute-intense parts of BigStitcher distributed

  Java

  •

  BSD 2-Clause "Simplified" License

  •13•26•15•3•Updated Aug 13, 2025Aug 13, 2025

• 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 into a single pipeline to reduce manual work and errors.

  Python

  •

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

  •0•5•0•1•Updated Aug 12, 2025Aug 12, 2025

• fileglancer

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

  TypeScript

  •

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

  •0•1•0•2•Updated Aug 12, 2025Aug 12, 2025

• neuronbridge-data

  Public
  Versioned NeuronBridge data files deployed to S3 buckets

  Python

  •

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

  •0•0•0•0•Updated Aug 12, 2025Aug 12, 2025

• easifish

  Public
  Nextflow

  •

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

  •0•0•0•0•Updated Aug 12, 2025Aug 12, 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 Aug 12, 2025Aug 12, 2025

• jrc_common

  Public
  Library of common utility functions for Python

  Python

  •

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

  •0•0•0•0•Updated Aug 12, 2025Aug 12, 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•2•Updated Aug 12, 2025Aug 12, 2025

• UInt12Arrays.jl

  Public
  Julia package for supporting arrays of 12-bit integers

  Julia

  •

  Other

  •0•9•1•1•Updated Aug 11, 2025Aug 11, 2025

• bigstream

  Public
  Tools for distributed alignment of massive images

  Jupyter Notebook

  •

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

  •21•85•13•4•Updated Aug 11, 2025Aug 11, 2025

• dis-utilities

  Public
  Utilities for Data and Information Services

  JavaScript

  •

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

  •1•2•14•1•Updated Aug 11, 2025Aug 11, 2025

• pydantic-ome-ngff

  Public
  Pydantic models for OME-NGFF

  Python

  •

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

  •3•24•6•1•Updated Aug 11, 2025Aug 11, 2025

• videoAnnotation

  Public
  JavaScript

  •

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

  •0•2•0•1•Updated Aug 11, 2025Aug 11, 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 Aug 11, 2025Aug 11, 2025

• jacs-tools

  Public
  Containerized image processing tools for JACS

  ImageJ Macro

  •

  Other

  •0•1•0•0•Updated Aug 10, 2025Aug 10, 2025

• containers

  Public
  Containers for workflow plugins

  Python

  •

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

  •0•0•0•0•Updated Aug 8, 2025Aug 8, 2025

• nf-omezarr

  Public
  Nextflow pipeline for converting images to OME-Zarr using bioformats2raw

  ome-zarr-converter

  Groovy

  •

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

  •0•1•0•0•Updated Aug 7, 2025Aug 7, 2025

• nextflow-modules

  Public
  Nextflow modules for use with nf-core tooling

  Nextflow

  •

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

  •0•1•0•0•Updated Aug 7, 2025Aug 7, 2025

• fileglancer-central

  Public
  Central metadata server for Fileglancer deployments

  Python

  •

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

  •0•0•0•0•Updated Aug 7, 2025Aug 7, 2025

• RubinFlyDiscoSettings

  Public
  Rubin Lab settings folder for FlyDiscoAnalysis

  Shell

  •0•0•0•0•Updated Aug 6, 2025Aug 6, 2025

• colormipsearch

  Public
  Distributed Color Depth MIP Search

  neurosciencesearch-algorithmneuron

  Java

  •

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

  •1•2•0•2•Updated Aug 6, 2025Aug 6, 2025

• transfero

  Public
  Python scripts for transferring data from rig computers

  Python

  •0•0•3•0•Updated Aug 5, 2025Aug 5, 2025

• videoAnnotation_backend

  Public
  Python

  •

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

  •0•0•0•0•Updated Aug 3, 2025Aug 3, 2025

• gpt-semantic-search

  Public
  Semantic search for Janelia resources using GPT models

  Python

  •

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

  •1•3•0•0•Updated Aug 1, 2025Aug 1, 2025

• phase-change

  Public
  archive data to cold storage

  Shell

  •

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

  •0•0•0•0•Updated Jul 31, 2025Jul 31, 2025

• tethered-fly-pipeline

  Public
  Nextflow pipeline for processing tethered fly videos using APT

  neurosciencejanelia

  Nextflow

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Jul 31, 2025Jul 31, 2025

• jacs-dashboard

  Public
  Dashboard interface for the JACSv2 services ecosystem.

  JavaScript

  •

  MIT License

  •0•0•4•4•Updated Jul 30, 2025Jul 30, 2025

• neuronbridge-python

  Public
  Python API for NeuronBridge

  Jupyter Notebook

  •

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

  •0•0•0•0•Updated Jul 30, 2025Jul 30, 2025