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https://github.com/janeliascicomp/awesome-janelia-software

A curated list of awesome Janelia software
https://github.com/janeliascicomp/awesome-janelia-software

List: awesome-janelia-software

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A curated list of awesome Janelia software

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# Awesome Janelia Software



[![Awesome](https://awesome.re/badge.svg)](https://awesome.re)



A curated list of awesome software actively maintained at Janelia. Inspired by various [awesome](https://github.com/sindresorhus/awesome) lists.



You can also browse Janelia software on the [Janelia OSSI Website](https://ossi.janelia.org).



### Contributing



Please read the [contribution guidelines](CONTRIBUTING.md).



### GitHub Organizations



* [Branson Lab](https://github.com/kristinbranson)

* [FlyEM](https://github.com/janelia-flyem)

* [FlyEM NeuPrint](https://github.com/connectome-neuprint)

* [Funkey Lab](https://github.com/funkey)

* [Johnson Lab](https://github.com/JohnsonLabJanelia)

* [Karpova Lab](https://github.com/Karpova-Lab)

* [Preibisch Lab](https://github.com/PreibischLab)

* [Reiser Lab](https://github.com/reiserlab)

* [Saalfeld Lab](https://github.com/saalfeldlab)

* [Scientific Computing](https://github.com/JaneliaSciComp)

* [Stringer and Pachitariu Labs](https://github.com/MouseLand)

* [Turaga Lab](https://github.com/TuragaLab)



## Containerization



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



* [Entrypoints](https://github.com/JaneliaSciComp/entrypoints) - Add multiple entrypoints into a Docker container

* [Maru](https://github.com/JaneliaSciComp/maru) - Command-line tool for containerizing scientific applications



## Data Services



*Systems for handling scientific data on the web or through APIs*



* [DVID](https://dvid.io) - Connectomics data service supporting branched versioning of data 

* [Clio](https://github.com/clio-janelia) - Connectomics website with a serverless data API service

* [Web H5J Loader](https://github.com/JaneliaSciComp/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](https://github.com/kristinbranson/APT) - Animal Part Tracker

* [CATMAID](https://catmaid.readthedocs.io/en/stable/) - Web application for collaborative neural circuit reconstruction and analysis

* [Cellpose](https://github.com/MouseLand/cellpose) - Deep learning tool for cell segmentation 

* [Facemap](https://github.com/mouseland/facemap) - mouse facial behavior analysis

* [G4 Display Tools](https://github.com/JaneliaSciComp/G4_Display_Tools) - Collection of tools for using Modular LED Displays (4th generation)

* [HippoSeq](https://hipposeq.janelia.org) - Interactive analysis tool for RNA-seq data in the mouse hippocampus

* [HortaCloud](https://hortacloud.janelia.org) - Cloud-based application for collaborative neuron tracing in large sparse volumes 

* [JAABA](https://github.com/kristinbranson/JAABA) - Janelia Animal Behavior Detector 

* [Janelia Workstation](https://github.com/JaneliaSciComp/workstation) - Data management platform supporting the FlyLight and MouseLight projects

* [Kilosort](https://github.com/MouseLand/Kilosort) - Pipeline for spike sorting multi-site electrophysiological recordings

* [neuPrint+](https://neuprint.janelia.org) - Analysis tools for connectomics

* [NeuronBridge](https://neuronbridge.janelia.org) - Web service for EM/LM neuron matching 

* [NeuroSeq](https://neuroseq.janelia.org) - Interactive analysis tool for RNA-seq data in the mouse

* [NeuTu](https://janelia-flyem.gitbook.io/neutu) - Software package for neuron reconstruction and visualization 

* [Paintera](https://github.com/saalfeldlab/paintera) - Visualization, proof-reading and manual annotation for large 3D image data

* [RAISIN](https://raisin.janelia.org) - Web application for *Rabies-Assisted Interrogation of Synaptic Infralimbic Networks*

* [Rastermap](https://github.com/mouseland/rastermap) - Non-linear manifold embedding algorithm for visualizing neural activity

* [SongExplorer](https://github.com/JaneliaSciComp/SongExplorer) - Deep learning for acoustic signals

* [Suite2p](https://github.com/mouseland/suite2p) - Pipeline for ROI detection and extraction in 2-photon recordings

* [VVD Viewer](https://github.com/JaneliaSciComp/VVDViewer) - Interactive 3D volume viewer for large microscopy data

* [WaveSurfer](https://wavesurfer.janelia.org) - An application for acquiring neurophysiology data



## Fiji Plugins



*Plugins for the [Fiji](https://fiji.sc) platform for scientific image analysis*



* [BigDataViewer](https://github.com/bigdataviewer/bigdataviewer_fiji) - Re-slicing browser for terabyte-sized multi-view image sequences

* [BigStitcher](https://github.com/PreibischLab/BigStitcher) - ImgLib2/BDV implementation of Stitching for large datasets

* [BigWarp](https://github.com/saalfeldlab/bigwarp) - Pointwise deformable 2D and 3D registration of large image data

* [ColorMIP Mask Search](https://github.com/JaneliaSciComp/ColorMIP_Mask_Search) - Fiji plugin for color depth search

* [H5J Loader](https://github.com/JaneliaSciComp/H5J_Loader_Plugin) - Fiji plugin for loading images in lossy H5J format

* [n5-ij](https://github.com/saalfeldlab/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](https://github.com/JaneliaSciComp/burst-compute) - AWS service for highly parallel Lambda processing

* [Daisy](https://github.com/funkelab/daisy) - Block-size task scheduling for large volumes

* [JACS](https://github.com/JaneliaSciComp/jacs-compute) - RESTful services for running jobs at scale

* [Java LSF](https://github.com/JaneliaSciComp/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](https://github.com/imglib/imglib2) ecosystem*



* [ImgLib2](https://github.com/imglib) - ImgLib2 project (lots of subprojects)

* [BigDataViewer](https://github.com/bigdataviewer) - Re-slicing browser for terabyte-sized multi-view image sequences

* [N5](https://github.com/saalfeldlab/n5) - Specification for the N5 file format

* [N5 Spark](https://github.com/saalfeldlab/n5-spark) - Tools for working with N5 on a Spark cluster

* [N5 Viewer](https://github.com/saalfeldlab/n5-viewer) - Viewer for visualizing N5 data sets

* [Render](https://github.com/saalfeldlab/render) - RESTful services for large image transformation and rendering

* [Hot-Knife](https://github.com/saalfeldlab/hot-knife) - ImgLib2 code for processing very large EM and Lightsheet data

* [Stitching Spark](https://github.com/saalfeldlab/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](https://github.com/GFleishman/ClusterWrap) - Python library for running Dask on the Janelia cluster

* [dask-janelia](https://github.com/JaneliaSciComp/dask-janelia) - Python library for running Dask on the Janelia cluster

* [Spark Janelia](https://github.com/JaneliaSciComp/spark-janelia) - Command line tool for running Spark on the Janelia cluster

* [ray-janelia](https://github.com/JaneliaSciComp/ray-janelia) - Python library for running Ray on the Janelia cluster



## Julia Packages



*Packages for the [Julia Programming Language](https://julialang.org/)*



* [UInt12Arrays](https://github.com/JaneliaSciComp/UInt12Arrays.jl) - Handle 12-bit unsigned integers in Julia with SIMD (AVX2 and AVX512) support

* [ImarisWriter](https://github.com/JaneliaSciComp/ImarisWriter.jl) - Julia API for writing files in Imaris5 file format

* [ClusterManagers](https://github.com/JuliaParallel/ClusterManagers.jl) - Contributed Julia support for interacting with IBM Platform LSF

* [Blosc2_jll](https://github.com/JuliaBinaryWrappers/Blosc2_jll.jl) - Contributed build script for cross-compilation of C-Blosc2



## Machine Learning



*Libraries for training and applying machine learning models*



* [DECODE](https://github.com/TuragaLab/DECODE) - Deep learning tool for single molecule localization microscopy (SMLM)

* [Gunpowder](https://github.com/funkey/gunpowder) - Library for machine learning on multi-dimensional images

* [DaCaPo](https://github.com/funkelab/dacapo/blob/attrs-dev/README.md) - Automatic parameter detection for deep learning



## Nextflow Pipelines



*Containerized analysis pipelines that run anywhere using the [Nextflow](https://www.nextflow.io) workflow system*



* [EASI-FISH Pipeline](https://github.com/JaneliaSciComp/multifish) - Spatial transcriptomics using the EASI-FISH protocol

* [ExLLSM Circuit Reconstruction Pipeline](https://github.com/JaneliaSciComp/exllsm-circuit-reconstruction) - Pipeline for analyzing ExM data with neuron/synapse segmentation

* [Nextflow Spark](https://github.com/JaneliaSciComp/nextflow-spark) - Spin up transient Spark clusters as part of a Nextflow pipeline

* [Nextflow Dask](https://github.com/JaneliaSciComp/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](https://github.com/GFleishman/bigstream) - Distributed piecewise affine and deformable alignment for big 3D datasets

* [CircuitSeeker](https://github.com/GFleishman/CircuitSeeker) - Distributed complex alignment tasks for big 4D datasets

* [FishSpot](https://github.com/GFleishman/fishspot) - Fully automated PSF estimation and spot detection for punctate data (e.g. FISH spots)

* [Python Dist Demo](https://github.com/JaneliaSciComp/python-dist-demo) - Examples of bundling Python scripts and dependencies into execultables for easy sharing

* [xarray-multiscale](https://github.com/JaneliaSciComp/xarray-multiscale) - Library for generating multiscale pyramids with Dask



## Visualization Tools



*Tools and libraries for 3D visualizations*



* [Blender Spherical Video](https://github.com/JaneliaSciComp/blender-spherical-video) - Scripts for rendering 360-degree spherical videos in Blender

* [Janelia Unity Toolkit](https://github.com/JaneliaSciComp/janelia-unity-toolkit) - Unity game engine packages enabling animal studies in VR

* [neuVid](https://github.com/connectome-neuprint/neuVid) - Generate biology videos from high-level descriptions using Blender and VVDViewer

* [VVD Viewer](https://github.com/JaneliaSciComp/VVDViewer) - Interactive 3D volume viewer for large microscopy data

* [Web Vol Viewer](https://github.com/JaneliaSciComp/web-vol-viewer) - Direct volume rendering in a browser using WebGL 2



## License



[![CC0 1.0 Universal (CC0 1.0) Public Domain Dedication ](https://i.creativecommons.org/p/zero/1.0/88x31.png)](https://creativecommons.org/publicdomain/zero/1.0/)

This work is licensed under a [CC0 1.0 Universal (CC0 1.0) Public Domain Dedication](https://creativecommons.org/publicdomain/zero/1.0/).