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bigstream
Tools for distributed alignment of massive imagesNIDAQ.jl
National Instruments Data Acquisition InterfaceJRCLUST
JRCLUSTmultifish
EASI-FISH analysis pipeline for spatial transcriptomicsxarray-multiscale
scalable multiscale image pyramids in pythonworkstation
Janelia WorkstationSharkViewer
SharkViewer is a web-based viewer for SWC neuron files. It is written entirely in JavaScript using Three.js.SongExplorer
deep learning for acoustic signalspydantic-ome-ngff
Pydantic models for OME-NGFFosgpyplusplus
Python bindings for OpenSceneGraph 3D graphics API, created using Boost.Python and Py++BigStitcher-Spark
Running compute-intense parts of BigStitcher distributedWavesurfer
A Matlab application for electrophysiology data analysisVVDViewer
3D/4D volumetric rendering of microscopy dataMorton.jl
convert between Z-order, Cartesian, and quadtree/octree coordinatesSymmetricFormats.jl
efficient storage for symmetric matricesnextflow-spark
exllsm-circuit-reconstruction
Nextflow pipeline encapsulating workflows for analyzing expansion lattice light-sheet microscopy (ExLLSM) imageryjanelia-unity-toolkit
Packages for the Unity game engine, emphasizing animal studies in VR.three-orbit-unlimited-controls
A THREE.js camera controller that improves on OrbitControls and TrackballControls.msg
Multiplexed Shotgun Genotypingweb-vol-viewer
Direct volume rendering with WebGL 2.Muse
Code for localization of mouse ultrasonic vocalizations using a microphone arrayJaneliaDataStandards
A pilot experiment to dissminate information about Janelia's biomaging data formats.hortacloud
HortaCloud - 3D annotation platform for large microscopy dataNeuroptikon
NeuroptikonUInt12Arrays.jl
Julia package for supporting arrays of 12-bit integersPyWaveSurfer
PyWaveSurfer is a Python package for reading WaveSurfer data files in Python.blender-spherical-video
Scripts for Blender to render 360-degree spherical videos.jacs-cm
JACS Configuration ManagementColorMIP_Mask_Search
ColorMIP_Mask_Search plugin for FijiKLEIO-Java-SDK
Versioned Storage Java SDK: Block based versioned data storage.CohenBolstadLee_eLife2017
VR System Released with eLife 2017 publication: "Experience-dependent shaping of hippocampal CA1 intracellular activity in novel and familiar environmentsβkeller-lab-block-filetype
Code related to image I/O API for the .klb file type. Briefly, images are split into blocks and each thread process the blocks independently for maximum parallelization. For storage, different compression algorithms can be used.maru
Maru is an opinionated command-line interface for quickly and easily containerizing scientific applications.neuronbridge
EM/LM neuron searchFlyoVeR
xarray-ome-ngff
Integration between xarray and the ome-ngff data model.DataPro
Package of Igor Pro scripts for doing data acquisition using Instrutech hardware.mipav
MIPAV (Medical Image Processing, Analysis, and Visualization), mirrored from https://citdcbmipav.cit.nih.gov/repos-pub/mipav/figleaf
Tool for data publication on figshare. Just getting off the ground.burst-compute
Burst compute framework for AWSBatchedBLAS.jl
batch what Nvidia does notblender-physics
Scripts to use Blender for physical simulations in pythonomnivore
record synchronized audio and videotmt
A toolbox of Matlab functions useful for data analysis, especially of electrophysiology data.aitch
local scheduler for heterogenous jobsjava-lsf
Java API to IBM Platform LSFLightsheet-Processing-Pipeline
Pipeline from Philipp Keller ([email protected]) and group to process light-sheet microscopy data. Originated here: https://www.janelia.org/lab/keller-lab/software/efficient-processing-and-analysis-large-scale-light-sheet-microscopy-dataKLEIO-Python-SDK
hortacloud-importer
a tiff-to-octree converter for dasktempo
Media browsing, analysis and annotationJaneliaGatherMap
Ax
Acoustic SegmenterG4_Display_Tools
Collection of tools for the G4 LED arena displays.SAM_service
Web service which generates Segment Anything modelsdlc-trainer
A service that trains DeepLabCut modelsjrc_intro_programming
Introduction to Python Programming @ Janelia Research Campusneuronbridge-services
AWS Services for NeuronBridgePointMatchExplorer
Point Match Explorer for FlyTEMTileAlignment
Alignment of the overlapping TEM images of the brainhortacloud-website
Documentation website for HortaCloudnf-demos
Nextflow Demo Pipelines for Image Processingray-janelia
Run Python Ray on the Janelia cluster2020AprilGitCourse
this repo supports the April 2020 git and GitHub course held "at" Janeliapeeling
multiscale-metadata
Guidelines for metadata for multiscale images stored in hierarchical storage schemes (e.g., Zarr / N5)image_processing_pipeline
Interface to configure pipeline jobs for LightSheetnf-rsfish
Nextflow wrapper for RS-FISH-SparkEM_recon_pipeline
Pipeline scripts and tools for reconstructing Electron Microscopy volumes.ImagingEcosystem
The Imaging Ecosystem (well, parts of it, anyway).web-h5j-loader
Lets browser apps load H5J data files.jacs-compute
JAnelia Compute Services (JACS)chunk-compression-benchmarks
Benchmarks for compressing chunked data of different flavorsjacs-model
JACS Domain Model and DAOsnextflow-dask
lightsheetrecon
TransformationBDV
BDV with transformation featuretpt
A tentative Python toolboxentrypoints
Support multiple entrypoint scripts in a container for use in containerized scientific tools.Kafka_examples
Example producer/consumer programs for Kafkajrc_programming_python_practicals
Practical's for the Introduction to Python Workshopvideo_grid
Display many small videos in a gridn5-zstandard
Zstandard Compression for N5jacs-tools
Containerized image processing tools for JACSneuronbridge-aligners
Containerized Brain/VNC aligners for NeuronBridgen5-tools-dask
Dask-based utilities to process N5 imagesn5-inspector
Inspector for NGFF-style containers supported by the N5 API (N5, HDF5, OME-Zarr)merscope-utilities
Utilities for MolBio MERSCOPE data transfer and processinggpt-semantic-search
Semantic search for Janelia resources using GPT modelsossi-website
Website showcasing Janelia Open Science Software Intiative (OSSI) supported software projects and other software developed at Janelia.jproxy
S3 Proxypython-dist-demo
Tests of bundling Python scripts and dependencies into stand-alone executables.Love Open Source and this site? Check out how you can help us