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awesome-janelia-software

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

Last synced: 5 days ago
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  • Data Services

    • Clio - Connectomics website with a serverless data API service
    • Web H5J Loader - Lets web applications load H5J data efficiently using WASM
    • DVID - Connectomics data service supporting branched versioning of data
    • 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

  • Containerization

    • Entrypoints - Add multiple entrypoints into a Docker container
    • Maru - Command-line tool for containerizing scientific applications

  • End-User Applications

    • APT - Animal Part Tracker
    • 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
    • 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
    • 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
    • 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
    • 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
    • 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
    • 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
    • WaveSurfer - An application for acquiring neurophysiology data
    • WaveSurfer - An application for acquiring neurophysiology data

  • Fiji Plugins

    • BigDataViewer - Re-slicing browser for terabyte-sized multi-view image sequences
    • BigStitcher - ImgLib2/BDV implementation of Stitching for large datasets
    • 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
    • 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
    • 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
    • n5-ij - Fiji plugin for loading and saving image data as N5 data sets

  • High Performance Computing

    • Burst Compute - AWS service for highly parallel Lambda processing
    • Daisy - Block-size task scheduling for large volumes
    • 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
    • JACS - RESTful services for running jobs at scale
    • Java LSF - Java library for interacting with a HPC compute cluster running IBM Platform LSF
    • Java LSF - Java library for interacting with a HPC compute cluster running IBM Platform LSF

  • ImgLib2, BDV and N5 Ecosystem

    • Imglib2
    • ImgLib2 - ImgLib2 project (lots of subprojects)
    • Imglib2
    • ImgLib2 - ImgLib2 project (lots of subprojects)
    • BigDataViewer - Re-slicing browser for terabyte-sized multi-view image sequences
    • 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 - 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
    • N5 Viewer - Viewer for visualizing N5 data sets
    • Render - RESTful services for large image transformation and rendering
    • 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
    • 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

    • ClusterWrap - Python library for running Dask on the Janelia cluster
    • dask-janelia - Python library for running Dask on the Janelia cluster
    • ClusterWrap - Python library for running Dask on the Janelia cluster
    • Spark Janelia - Command line tool for running Spark 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
    • ray-janelia - Python library for running Ray on the Janelia cluster

  • Julia Packages

  • Machine Learning

    • 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
    • Gunpowder - Library for machine learning on multi-dimensional images
    • DaCaPo - Automatic parameter detection for deep learning
    • Gunpowder - Library for machine learning on multi-dimensional images

  • Nextflow Pipelines

  • Python Libraries

    • BigStream - Distributed piecewise affine and deformable alignment for big 3D datasets
    • 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)
    • 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
    • Python Dist Demo - Examples of bundling Python scripts and dependencies into execultables for easy sharing
    • xarray-multiscale - Library for generating multiscale pyramids with Dask
    • BigStream - Distributed piecewise affine and deformable alignment for big 3D datasets

  • Visualization Tools

    • Blender Spherical Video - Scripts for rendering 360-degree spherical videos in Blender
    • Blender Spherical Video - Scripts for rendering 360-degree spherical videos in Blender
    • Janelia Unity Toolkit - Unity game engine packages enabling animal studies in VR
    • Janelia Unity Toolkit - Unity game engine packages enabling animal studies in VR
    • neuVid - Generate biology videos from high-level descriptions using Blender and VVDViewer
    • neuVid - Generate biology videos from high-level descriptions using Blender and VVDViewer
    • Web Vol Viewer - Direct volume rendering in a browser using WebGL 2
    • Web Vol Viewer - Direct volume rendering in a browser using WebGL 2
    • VVD Viewer - Interactive 3D volume viewer for large microscopy data
    • VVD Viewer - Interactive 3D volume viewer for large microscopy data
Programming Languages
Java 32 Python 29 Jupyter Notebook 9 Julia 8 Nextflow 6 MATLAB 6 JavaScript 6 Shell 4 C++ 2 C# 2
Categories
End-User Applications 40 ImgLib2, BDV and N5 Ecosystem 18 Fiji Plugins 12 Python Libraries 11 Visualization Tools 10 Julia Packages 10 High Performance Computing 8 Nextflow Pipelines 8 Janelia Site-specific Software 7 Machine Learning 6 Data Services 6 License 4 Containerization 2
Sub Categories
Keywords
neuroscience 14 pipeline 7 janelia 6 hpc 5 microscopy 5 machine-learning 5 neuroimaging 4 distributed-computing 4 segmentation 4 cluster 4 computer-vision 3 gunpowder 3 multidimensional 3 deep-learning 3 pytorch 3 scientific-computing 3 confocal-microscopy 2 connectomics 2 rodents 2 volume-rendering 2 electrophysiology 2 spike-sorting 2 neuroscience-methods 2 unsupervised-clustering 2 data-analysis 2 python 2 pupil 2 pose-estimation 2 movie 2 matlab-gui 2 gui 2 behavior 2 cell-segmentation 2 cell-biology 2 vvd-viewer 2 rendering 2 nextflow-pipelines 2 lightsheet 2 image-processing 2 nextflow 2 ibm-platform-lsf 2 easi-fish 2 ray 2 compute-clusters 2 lsf 2 docker 2 imaging 2 fiji 2 fiji-plugin 2 hdf5 2