Repositories list

• EM_recon_pipeline

  Public
  Pipeline scripts and tools for reconstructing Electron Microscopy volumes.

  Python

  •

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

  •2•4•0•3•Updated Nov 25, 2024Nov 25, 2024

• bigstream

  Public
  Tools for distributed alignment of massive images

  Jupyter Notebook

  •

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

  •21•75•11•2•Updated Nov 24, 2024Nov 24, 2024

• 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 Nov 23, 2024Nov 23, 2024

• videoAnnotation

  Public
  JavaScript

  •

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

  •0•0•0•0•Updated Nov 22, 2024Nov 22, 2024

• videoAnnotation_backend

  Public
  Python

  •

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

  •0•0•0•0•Updated Nov 22, 2024Nov 22, 2024

• dis-utilities

  Public
  Utilities for Data and Information Services

  JavaScript

  •

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

  •1•0•22•1•Updated Nov 22, 2024Nov 22, 2024

• janelia-unity-toolkit

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

  C#

  •

  Other

  •11•16•5•2•Updated Nov 22, 2024Nov 22, 2024

• neuronbridge-python

  Public
  Python API for NeuronBridge

  Jupyter Notebook

  •

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

  •0•0•0•0•Updated Nov 21, 2024Nov 21, 2024

• JaneliaDataStandards

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

  HTML

  •

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

  •2•10•2•3•Updated Nov 21, 2024Nov 21, 2024

• 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 Nov 21, 2024Nov 21, 2024

• jacs-compute

  Public
  JAnelia Compute Services (JACS)

  distributed-computingneuroimagingcluster-computing

  Java

  •

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

  •0•1•0•0•Updated Nov 20, 2024Nov 20, 2024

• colormipsearch

  Public
  Distributed Color Depth MIP Search

  neurosciencesearch-algorithmneuron

  Java

  •

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

  •1•0•0•2•Updated Nov 20, 2024Nov 20, 2024

• jrc_common

  Public
  Library of common utility functions for Python

  Python

  •

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

  •0•0•0•0•Updated Nov 19, 2024Nov 19, 2024

• ImagingEcosystem

  Public
  The Imaging Ecosystem (well, parts of it, anyway).

  Perl

  •0•1•1•1•Updated Nov 19, 2024Nov 19, 2024

• neuronbridge

  Public
  EM/LM neuron search

  neuroscienceneuroimagingneurons+ 3drosophilajaneliaaws

  JavaScript

  •

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

  •1•4•0•8•Updated Nov 19, 2024Nov 19, 2024

• ShroffCelegansModels.jl

  Public
  Julia

  •

  MIT License

  •0•2•0•35•Updated Nov 19, 2024Nov 19, 2024

• VVDViewer

  Public
  3D/4D volumetric rendering of microscopy data

  renderingneurosciencemicroscopy+ 1vvd-viewer

  C++

  •

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

  •5•20•3•1•Updated Nov 18, 2024Nov 18, 2024

• multifish

  Public
  EASI-FISH analysis pipeline for spatial transcriptomics

  nextfloweasi-fishibm-platform-lsf+ 1pipeline

  Jupyter Notebook

  •

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

  •14•33•19•0•Updated Nov 18, 2024Nov 18, 2024

• pydantic-ome-ngff

  Public
  Pydantic models for OME-NGFF

  Python

  •

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

  •3•21•6•1•Updated Nov 18, 2024Nov 18, 2024

• hortacloud-importer

  Public
  a tiff-to-octree converter for dask

  Python

  •

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

  •2•2•0•0•Updated Nov 15, 2024Nov 15, 2024

• FunkeAnnotation

  Public
  Small tool to annotate images

  Java

  •0•0•0•0•Updated Nov 15, 2024Nov 15, 2024

• x2s3

  Public
  S3 Proxy Service

  s3s3-buckets3-storage

  Python

  •

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

  •0•6•0•1•Updated Nov 15, 2024Nov 15, 2024

• exllsm-neuron-segmentation

  Public
  Neuron segmentation for expanded microscopy

  Python

  •

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

  •1•0•0•0•Updated Nov 15, 2024Nov 15, 2024

• workstation

  Public
  Janelia Workstation

  neurosciencescientific-computingneuroimaging+ 4volume-renderingconnectomicsjaneliaconfocal-microscopy

  Java

  •

  Other

  •11•23•0•11•Updated Nov 14, 2024Nov 14, 2024

• RubinFlyDiscoSettings

  Public
  Rubin Lab settings folder for FlyDiscoAnalysis

  Shell

  •0•0•0•0•Updated Nov 14, 2024Nov 14, 2024

• SongExplorer

  Public
  deep learning for acoustic signals

  Python

  •

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

  •5•23•5•1•Updated Nov 13, 2024Nov 13, 2024

• 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

  •17•1•16•1•Updated Nov 12, 2024Nov 12, 2024

• zarrcade

  Public
  Create web-based OME-Zarr galleries

  webappmicroscopy-imagesome-zarr

  Jupyter Notebook

  •

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

  •0•10•3•0•Updated Nov 9, 2024Nov 9, 2024

• BigStitcher-Spark

  Public
  Running compute-intense parts of BigStitcher distributed

  Java

  •

  BSD 2-Clause "Simplified" License

  •11•20•15•1•Updated Nov 8, 2024Nov 8, 2024

• PyWaveSurfer

  Public
  PyWaveSurfer is a Python package for reading WaveSurfer data files in Python.

  Python

  •6•9•1•7•Updated Nov 8, 2024Nov 8, 2024