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 Jan 31, 2026Jan 31, 2026

• easifish

  Public
  Nextflow

  •

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

  •0•1•0•0•Updated Jan 31, 2026Jan 31, 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 Jan 30, 2026Jan 30, 2026

• dis-utilities

  Public
  Utilities for Data and Information Services

  JavaScript

  •

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

  •1•2•14•1•Updated Jan 30, 2026Jan 30, 2026

• jrc_common

  Public
  Library of common utility functions for Python

  Python

  •

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

  •0•0•0•0•Updated Jan 30, 2026Jan 30, 2026

• 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 Jan 30, 2026Jan 30, 2026

• bigstream

  Public
  Tools for distributed alignment of massive images

  Jupyter Notebook

  •

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

  •22•92•13•3•Updated Jan 30, 2026Jan 30, 2026

• jacs-dashboard

  Public
  Dashboard interface for the JACSv2 services ecosystem.

  JavaScript

  •

  MIT License

  •0•0•4•13•Updated Jan 30, 2026Jan 30, 2026

• fileglancer

  Public
  Browse, share, and publish OME-Zarr data

  microscopyimagingzarr+ 3ngffome-zarrome-ngff

  TypeScript

  •

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

  •2•17•0•5•Updated Jan 30, 2026Jan 30, 2026

• doi_common

  Public
  Library of common DOI-related functions for Python

  Python

  •

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

  •0•0•0•0•Updated Jan 30, 2026Jan 30, 2026

• BigStitcher-Spark

  Public
  Running compute-intense parts of BigStitcher distributed

  Java

  •

  BSD 2-Clause "Simplified" License

  •17•29•18•2•Updated Jan 30, 2026Jan 30, 2026

• neuronbridge

  Public
  EM/LM neuron search

  awsneuroscienceneuroimaging+ 3neuronsdrosophilajanelia

  JavaScript

  •

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

  •1•5•0•17•Updated Jan 28, 2026Jan 28, 2026

• hortacloud

  Public
  HortaCloud - 3D annotation platform for large microscopy data

  awsneurosciencescientific-computing+ 3neuronsannotation-tooljanelia

  JavaScript

  •

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

  •1•10•49•0•Updated Jan 28, 2026Jan 28, 2026

• containers

  Public
  Containers for workflow plugins

  Python

  •

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

  •0•0•0•1•Updated Jan 28, 2026Jan 28, 2026

• neuronbridge-python

  Public
  Python API for NeuronBridge

  Jupyter Notebook

  •

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

  •0•0•1•0•Updated Jan 27, 2026Jan 27, 2026

• SoundLocalizer

  Public
  find the source using a microphone array

  Julia

  •

  Other

  •0•0•0•0•Updated Jan 26, 2026Jan 26, 2026

• cellpose-tools

  Public
  Python code for the nf-cellpose pipeline

  Python

  •

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

  •0•0•0•0•Updated Jan 26, 2026Jan 26, 2026

• fileglancer-docs

  Public
  Fileglancer user documentation site

  MDX

  •

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

  •0•0•0•5•Updated Jan 23, 2026Jan 23, 2026

• workstation

  Public
  Janelia Workstation

  neurosciencescientific-computingneuroimaging+ 4volume-renderingconnectomicsjaneliaconfocal-microscopy

  Java

  •

  Other

  •12•25•1•13•Updated Jan 23, 2026Jan 23, 2026

• fileglancer-hub

  Public
  Production deployment scripts for Fileglancer

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

  •0•0•0•0•Updated Jan 23, 2026Jan 23, 2026

• configurator

  Public
  JavaScript

  •

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

  •0•0•0•0•Updated Jan 21, 2026Jan 21, 2026

• claude-howto

  Public
  Shell

  •0•2•0•0•Updated Jan 16, 2026Jan 16, 2026

• micropattern_cell_analysis

  Public
  Micropattern Cell Analysis for the Gladkova and Vale Labs

  Python

  •

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

  •0•0•0•0•Updated Jan 16, 2026Jan 16, 2026

• SOFIMA-scripts

  Public
  wrapper to batch jobs to cluster

  Python

  •

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

  •1•1•0•0•Updated Jan 15, 2026Jan 15, 2026

• G4_Display_Tools

  Public
  Collection of tools for the G4 LED arena displays.

  MATLAB

  •

  Creative Commons Attribution 4.0 International

  •5•2•12•0•Updated Jan 15, 2026Jan 15, 2026

• easifish-spots-tools

  Public
  Various tools used by EASI-FISH pipeline for processing spots

  Python

  •0•0•0•0•Updated Jan 14, 2026Jan 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

  •24•31•30•7•Updated Jan 13, 2026Jan 13, 2026

• ShroffCelegansModels.jl

  Public
  Julia

  •

  MIT License

  •1•3•0•43•Updated Jan 13, 2026Jan 13, 2026

• neuronbridge-services

  Public
  AWS Services for NeuronBridge

  JavaScript

  •

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

  •1•2•0•18•Updated Jan 12, 2026Jan 12, 2026

• flycore-utilities

  Public
  Utility programs for synchronization with the Fly Facility's FLYF2 database

  Python

  •

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

  •0•1•0•0•Updated Jan 12, 2026Jan 12, 2026