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
- Johnson Lab
- Karpova Lab
- Preibisch Lab
- Reiser Lab
- Saalfeld Lab
- Scientific Computing
- Stringer and Pachitariu Labs
- Turaga Lab
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
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
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
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
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
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
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
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
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
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 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
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
