Awesome Janelia Software

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

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

EASI-FISH Pipeline - Spatial transcriptomics using the EASI-FISH protocol
ExLLSM Circuit Reconstruction Pipeline - Pipeline for analyzing ExM data with neuron/synapse segmentation
Nextflow Spark - Spin up transient Spark clusters as part of a Nextflow pipeline
Nextflow Dask - Spin up transient Dask clusters as part of a Nextflow pipeline

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

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

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