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
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
- dask-janelia - Library for running Dask on the Janelia cluster
- xarray-multiscale - Library for generating multiscale pyramids with Dask
Scientific applications with GUIs and user manuals
- 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
- 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 an HPC compute cluster running IBM Platform LSF
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
