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

Please read the contribution guidelines.

• Branson Lab
• FlyEM
• FlyEM NeuPrint
• Funkey Lab
• Preibisch Lab
• Saalfeld Lab
• Scientific Computing Software
• Stringer Lab
• Turaga Lab

Computer vision tools for animal behavior

• APT - Animal Part Tracker
• JAABA - Janelia Animal Behavior Detector

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

Image processing in the Dask/Python ecosystem

• ClusterWrap - Library for running Dask on the Janelia cluster
• dask-janelia - Library for running Dask on the Janelia cluster
• xarray-multiscale - Library for generating multiscale pyramids with Dask

Systems for handling scientific data on the web or through APIs

• DVID - A Connectomics data service that supports branched versioning of data and a variety of storage backends
• Clio - Software for a Connectomics website with a serverless data API service

Scientific applications with GUIs and user manuals

• 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)
• HippoSeq - Interactive analysis tool for RNA-seq data in the mouse hippocampus
• Janelia Workstation - Discovery platform supporting the FlyLight and MouseLight projects
• neuPrint+ - Analysis tools for connectomics
• NeuronBridge - EM/LM correspondence searches
• NeuroSeq - Interactive analysis tool for RNA-seq data in the mouse
• NeuTu - Software package for neuron reconstruction and visualization
• RAISIN - Web site for Rabies-Assisted Interrogation of Synaptic Infralimbic Networks
• SongExplorer - Deep learning for acoustic signals
• VVD Viewer - Interactive 3D volume viewer for large microscopy data

Plugins for Fiji

• BigStitcher - ImgLib2/BDV implementation of Stitching for large datasets
• 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

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

Packages for the Julia Language

• UInt12Arrays.jl - Handle 12-bit unsigned integers in Julia with SIMD (AVX2 and AVX512) support
• ImarisWriter.jl - Julia bindings for ImarisWriter. See also the Janelia development fork of ImarisWriter as well as a binary distribution, ImarisWriter_jll.jl, of that fork via BinaryBuilder.org.

Janelia Scientific Computing also contributed to the following Julia packages.

• ClusterManagers.jl - Contributed Julia support for interacting with a HPC compute cluster running IBM Platform LSF
• Blosc2_jll.jl - Contributed build script for cross-compilation of C-Blosc2 binaries via BinaryBuilder.org.

Libraries for training and applying machine learning models

• Cellpose - Deep learning tool for cell segmentation
• DECODE - Deep learning tool for single molecule localization microscopy (SMLM)
• Gunpowder - Library for machine learning on multi-dimensional images

Image processing tools in the N5/Imglib2 ecosystem

• N5 - 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
• Stitching Spark - Reconstruct large images from overlapping tiles on a Spark cluster

Containerized analysis pipelines that run anywhere.

• EASI-FISH Pipeline - for spatial transcriptomics using EASI-FISH
• ExM Pipeline - Pipeline for analyzing ExM data with neuron/synapse segmentation
• Nextflow Spark - library for including Spark clusters as part of a Nextflow pipeline

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 connectome videos from high-level descriptions using Blender

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