Repositories list

• easifish

  Public
  Nextflow

  •

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

  •0•0•0•0•Updated Jan 29, 2025Jan 29, 2025

• containers

  Public
  Containers for workflow plugins

  Python

  •

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

  •0•0•0•0•Updated Jan 29, 2025Jan 29, 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 Jan 29, 2025Jan 29, 2025

• JaneliaDataStandards

  Public
  A pilot experiment to dissminate information about Janelia's biomaging data formats.

  HTML

  •

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

  •3•11•3•3•Updated Jan 29, 2025Jan 29, 2025

• hortacloud-website

  Public
  Documentation website for HortaCloud

  neurosciencejaneliahortacloud

  HTML

  •

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

  •0•2•0•3•Updated Jan 29, 2025Jan 29, 2025

• BigStitcher-Spark

  Public
  Running compute-intense parts of BigStitcher distributed

  Java

  •

  BSD 2-Clause "Simplified" License

  •12•21•15•1•Updated Jan 29, 2025Jan 29, 2025

• SongExplorer

  Public
  deep learning for acoustic signals

  Python

  •

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

  •6•24•5•1•Updated Jan 28, 2025Jan 28, 2025

• jrc_common

  Public
  Library of common utility functions for Python

  Python

  •

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

  •0•0•0•0•Updated Jan 28, 2025Jan 28, 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 Jan 28, 2025Jan 28, 2025

• jacs-cm

  Public
  JACS Configuration Management

  janeliajanelia-workstationmouselight+ 4dockerdevopsdocker-swarmswarm

  XSLT

  •

  Other

  •3•8•17•2•Updated Jan 28, 2025Jan 28, 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 Jan 28, 2025Jan 28, 2025

• workstation

  Public
  Janelia Workstation

  neurosciencescientific-computingneuroimaging+ 4volume-renderingconnectomicsjaneliaconfocal-microscopy

  Java

  •

  Other

  •11•24•0•12•Updated Jan 27, 2025Jan 27, 2025

• pydantic-ome-ngff

  Public
  Pydantic models for OME-NGFF

  Python

  •

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

  •3•22•6•1•Updated Jan 27, 2025Jan 27, 2025

• jacs-compute

  Public
  JAnelia Compute Services (JACS)

  distributed-computingneuroimagingcluster-computing

  Java

  •

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

  •0•1•0•0•Updated Jan 27, 2025Jan 27, 2025

• jacs-storage

  Public
  JADE file storage services

  Java

  •

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

  •0•0•0•1•Updated Jan 27, 2025Jan 27, 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•4•Updated Jan 27, 2025Jan 27, 2025

• zarrcade

  Public
  Create web-based OME-Zarr galleries

  webappmicroscopy-imagesome-zarr

  Jupyter Notebook

  •

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

  •0•12•3•0•Updated Jan 25, 2025Jan 25, 2025

• neuronbridge

  Public
  EM/LM neuron search

  neuroscienceneuroimagingneurons+ 3drosophilajaneliaaws

  JavaScript

  •

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

  •1•4•0•10•Updated Jan 24, 2025Jan 24, 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 Jan 24, 2025Jan 24, 2025

• fileglancer

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

  TypeScript

  •

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

  •0•0•2•1•Updated Jan 24, 2025Jan 24, 2025

• dis-utilities

  Public
  Utilities for Data and Information Services

  JavaScript

  •

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

  •1•0•11•1•Updated Jan 24, 2025Jan 24, 2025

• G4_Display_Tools

  Public
  Collection of tools for the G4 LED arena displays.

  MATLAB

  •

  Creative Commons Attribution 4.0 International

  •3•2•10•0•Updated Jan 23, 2025Jan 23, 2025

• n5-utils

  Public
  simple standalone BigDataViewer for multiple N5 (or HDF5) datasets

  Java

  •

  Other

  •18•0•0•0•Updated Jan 23, 2025Jan 23, 2025

• jacs-model

  Public
  JACS Domain Model and DAOs

  Java

  •

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

  •0•1•0•0•Updated Jan 23, 2025Jan 23, 2025

• videoAnnotation

  Public
  JavaScript

  •

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

  •0•0•0•0•Updated Jan 21, 2025Jan 21, 2025

• n5-universe

  Public
  Functionality shared across all n5

  Java

  •

  BSD 2-Clause "Simplified" License

  •5•0•0•0•Updated Jan 21, 2025Jan 21, 2025

• exllsm-circuit-reconstruction

  Public
  Nextflow pipeline encapsulating workflows for analyzing expansion lattice light-sheet microscopy (ExLLSM) imagery

  neurosciencemicroscopylightsheet+ 5nextflow-pipelinesmachine-learningpipelineimage-processingsegmentation

  Nextflow

  •

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

  •1•13•2•0•Updated Jan 19, 2025Jan 19, 2025

• neuronbridge-services

  Public
  AWS Services for NeuronBridge

  JavaScript

  •

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

  •1•2•0•18•Updated Jan 15, 2025Jan 15, 2025

• janelia-unity-toolkit

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

  C#

  •

  Other

  •11•16•5•2•Updated Jan 15, 2025Jan 15, 2025

• bigstream

  Public
  Tools for distributed alignment of massive images

  Jupyter Notebook

  •

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

  •21•79•11•2•Updated Jan 15, 2025Jan 15, 2025