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Awesome Janelia Software

Awesome

A curated list of awesome software actively maintained at Janelia. Inspired by various awesome lists.

You can also browse Janelia software on the Janelia OSSI Website.

Contributing

Please read the contribution guidelines.

GitHub Organizations

Containerization

Tools for containerization and running containers (e.g. using Docker and Singularity)

  • Entrypoints - Add multiple entrypoints into a Docker container
  • Maru - Command-line tool for containerizing scientific applications

Data Services

Systems for handling scientific data on the web or through APIs

  • DVID - Connectomics data service supporting branched versioning of data
  • Clio - Connectomics website with a serverless data API service
  • Web H5J Loader - Lets web applications load H5J data efficiently using WASM

End-User Applications

Scientific applications (native or web) with GUIs and user manuals

  • APT - Animal Part Tracker
  • CATMAID - Web application for collaborative neural circuit reconstruction and analysis
  • Cellpose - Deep learning tool for cell segmentation
  • Facemap - mouse facial behavior analysis
  • G4 Display Tools - Collection of tools for using Modular LED Displays (4th generation)
  • HippoSeq - Interactive analysis tool for RNA-seq data in the mouse hippocampus
  • HortaCloud - Cloud-based application for collaborative neuron tracing in large sparse volumes
  • JAABA - Janelia Animal Behavior Detector
  • Janelia Workstation - Data management platform supporting the FlyLight and MouseLight projects
  • Kilosort - Pipeline for spike sorting multi-site electrophysiological recordings
  • neuPrint+ - Analysis tools for connectomics
  • NeuronBridge - Web service for EM/LM neuron matching
  • NeuroSeq - Interactive analysis tool for RNA-seq data in the mouse
  • NeuTu - Software package for neuron reconstruction and visualization
  • Paintera - Visualization, proof-reading and manual annotation for large 3D image data
  • RAISIN - Web application for Rabies-Assisted Interrogation of Synaptic Infralimbic Networks
  • Rastermap - Non-linear manifold embedding algorithm for visualizing neural activity
  • SongExplorer - Deep learning for acoustic signals
  • Suite2p - Pipeline for ROI detection and extraction in 2-photon recordings
  • VVD Viewer - Interactive 3D volume viewer for large microscopy data
  • WaveSurfer - An application for acquiring neurophysiology data

Fiji Plugins

Plugins for the Fiji platform for scientific image analysis

  • BigDataViewer - Re-slicing browser for terabyte-sized multi-view image sequences
  • BigStitcher - ImgLib2/BDV implementation of Stitching for large datasets
  • BigWarp - Pointwise deformable 2D and 3D registration of large image data
  • ColorMIP Mask Search - Fiji plugin for color depth search
  • H5J Loader - Fiji plugin for loading images in lossy H5J format
  • n5-ij - Fiji plugin for loading and saving image data as N5 data sets

High Performance Computing

Libraries and APIs for high-performance scientific computing on clusters and clouds

  • Burst Compute - AWS service for highly parallel Lambda processing
  • Daisy - Block-size task scheduling for large volumes
  • JACS - RESTful services for running jobs at scale
  • Java LSF - Java library for interacting with a HPC compute cluster running IBM Platform LSF

ImgLib2, BDV and N5 Ecosystem

Image processing tools in the Imglib2 ecosystem

  • ImgLib2 - ImgLib2 project (lots of subprojects)
  • BigDataViewer - Re-slicing browser for terabyte-sized multi-view image sequences
  • N5 - Specification for the N5 file format
  • N5 Spark - Tools for working with N5 on a Spark cluster
  • N5 Viewer - Viewer for visualizing N5 data sets
  • Render - RESTful services for large image transformation and rendering
  • Hot-Knife - ImgLib2 code for processing very large EM and Lightsheet data
  • Stitching Spark - Reconstruct large images from overlapping tiles on a Spark cluster

Janelia Site-specific Software

Packages that are intended to run with access to Janelia's internal network, but could be modified to work elsewhere

  • ClusterWrap - Python library for running Dask on the Janelia cluster
  • dask-janelia - Python library for running Dask on the Janelia cluster
  • Spark Janelia - Command line tool for running Spark on the Janelia cluster
  • ray-janelia - Python library for running Ray on the Janelia cluster

Julia Packages

Packages for the Julia Programming Language

  • UInt12Arrays - Handle 12-bit unsigned integers in Julia with SIMD (AVX2 and AVX512) support
  • ImarisWriter - Julia API for writing files in Imaris5 file format
  • ClusterManagers - Contributed Julia support for interacting with IBM Platform LSF
  • Blosc2_jll - Contributed build script for cross-compilation of C-Blosc2

Machine Learning

Libraries for training and applying machine learning models

  • DECODE - Deep learning tool for single molecule localization microscopy (SMLM)
  • Gunpowder - Library for machine learning on multi-dimensional images
  • DaCaPo - Automatic parameter detection for deep learning

Nextflow Pipelines

Containerized analysis pipelines that run anywhere using the Nextflow workflow system

Python Libraries

Python packages that can be installed with pip or conda

  • BigStream - Distributed piecewise affine and deformable alignment for big 3D datasets
  • CircuitSeeker - Distributed complex alignment tasks for big 4D datasets
  • FishSpot - Fully automated PSF estimation and spot detection for punctate data (e.g. FISH spots)
  • Python Dist Demo - Examples of bundling Python scripts and dependencies into execultables for easy sharing
  • xarray-multiscale - Library for generating multiscale pyramids with Dask

Visualization Tools

Tools and libraries for 3D visualizations

  • Blender Spherical Video - Scripts for rendering 360-degree spherical videos in Blender
  • Janelia Unity Toolkit - Unity game engine packages enabling animal studies in VR
  • neuVid - Generate biology videos from high-level descriptions using Blender and VVDViewer
  • VVD Viewer - Interactive 3D volume viewer for large microscopy data
  • Web Vol Viewer - Direct volume rendering in a browser using WebGL 2

License

CC0 1.0 Universal (CC0 1.0) Public Domain Dedication This work is licensed under a CC0 1.0 Universal (CC0 1.0) Public Domain Dedication.