Discover JaneliaSciComp/ossi-website Open Source project

National Instruments Data Acquisition Interface

NIDAQ.jl

JRCLUST

EASI-FISH analysis pipeline for spatial transcriptomics

multifish

scalable multiscale image pyramids in python

xarray-multiscale

workstation

Janelia Workstation

SharkViewer is a web-based viewer for SWC neuron files. It is written entirely in JavaScript using Three.js.

SharkViewer

deep learning for acoustic signals

SongExplorer

Pydantic models for OME-NGFF

pydantic-ome-ngff

Python bindings for OpenSceneGraph 3D graphics API, created using Boost.Python and Py++

osgpyplusplus

Running compute-intense parts of BigStitcher distributed

BigStitcher-Spark

A Matlab application for electrophysiology data analysis

Wavesurfer

3D/4D volumetric rendering of microscopy data

VVDViewer

convert between Z-order, Cartesian, and quadtree/octree coordinates

Morton.jl

efficient storage for symmetric matrices

SymmetricFormats.jl

A curated list of awesome Janelia software

awesome-janelia-software

nextflow-spark

Nextflow pipeline encapsulating workflows for analyzing expansion lattice light-sheet microscopy (ExLLSM) imagery

exllsm-circuit-reconstruction

Packages for the Unity game engine, emphasizing animal studies in VR.

janelia-unity-toolkit

three-orbit-unlimited-controls

A THREE.js camera controller that improves on OrbitControls and TrackballControls.

Multiplexed Shotgun Genotyping

msg

Direct volume rendering with WebGL 2.

web-vol-viewer

Code for localization of mouse ultrasonic vocalizations using a microphone array

Muse

A pilot experiment to dissminate information about Janelia's biomaging data formats.

JaneliaDataStandards

HTML

hortacloud

HortaCloud - 3D annotation platform for large microscopy data

Neuroptikon

Julia package for supporting arrays of 12-bit integers

UInt12Arrays.jl

PyWaveSurfer is a Python package for reading WaveSurfer data files in Python.

PyWaveSurfer

Scripts for Blender to render 360-degree spherical videos.

blender-spherical-video

JACS Configuration Management

jacs-cm

XSLT

ColorMIP_Mask_Search

ColorMIP_Mask_Search plugin for Fiji

ImageJ Macro

KLEIO-Java-SDK

Versioned Storage Java SDK: Block based versioned data storage.

VR System Released with eLife 2017 publication: "Experience-dependent shaping of hippocampal CA1 intracellular activity in novel and familiar environments”

CohenBolstadLee_eLife2017

keller-lab-block-filetype

Maru is an opinionated command-line interface for quickly and easily containerizing scientific applications.

maru

neuronbridge

EM/LM neuron search

FlyoVeR

Integration between xarray and the ome-ngff data model.

xarray-ome-ngff

Package of Igor Pro scripts for doing data acquisition using Instrutech hardware.

DataPro

IGOR Pro

mipav

MIPAV (Medical Image Processing, Analysis, and Visualization), mirrored from https://citdcbmipav.cit.nih.gov/repos-pub/mipav/

Tool for data publication on figshare. Just getting off the ground.

figleaf

Burst compute framework for AWS

burst-compute

batch what Nvidia does not

BatchedBLAS.jl

Scripts to use Blender for physical simulations in python

blender-physics

record synchronized audio and video

omnivore

A toolbox of Matlab functions useful for data analysis, especially of electrophysiology data.

tmt

local scheduler for heterogenous jobs

aitch

Rust

java-lsf

Java API to IBM Platform LSF

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-data

Lightsheet-Processing-Pipeline

KLEIO-Python-SDK

a tiff-to-octree converter for dask

hortacloud-importer

Media browsing, analysis and annotation

tempo

JaneliaGatherMap

Acoustic Segmenter

Collection of tools for the G4 LED arena displays.

G4_Display_Tools

Web service which generates Segment Anything models

SAM_service

A service that trains DeepLabCut models

dlc-trainer

Introduction to Python Programming @ Janelia Research Campus

jrc_intro_programming

AWS Services for NeuronBridge

neuronbridge-services

Point Match Explorer for FlyTEM

PointMatchExplorer

Alignment of the overlapping TEM images of the brain

TileAlignment

Documentation website for HortaCloud

hortacloud-website

HTML

nf-demos

Nextflow Demo Pipelines for Image Processing

Run Python Ray on the Janelia cluster

ray-janelia

Shell

2020AprilGitCourse

this repo supports the April 2020 git and GitHub course held "at" Janelia

peeling

Guidelines for metadata for multiscale images stored in hierarchical storage schemes (e.g., Zarr / N5)

multiscale-metadata

image_processing_pipeline

Interface to configure pipeline jobs for LightSheet

Nextflow wrapper for RS-FISH-Spark

nf-rsfish

Pipeline scripts and tools for reconstructing Electron Microscopy volumes.

EM_recon_pipeline

The Imaging Ecosystem (well, parts of it, anyway).

ImagingEcosystem

Perl

web-h5j-loader

Lets browser apps load H5J data files.

JAnelia Compute Services (JACS)

jacs-compute

Benchmarks for compressing chunked data of different flavors

chunk-compression-benchmarks

jacs-model

JACS Domain Model and DAOs

nextflow-dask

lightsheetrecon

BDV with transformation feature

TransformationBDV

A tentative Python toolbox

tpt

Support multiple entrypoint scripts in a container for use in containerized scientific tools.

entrypoints

Kafka_examples

Example producer/consumer programs for Kafka

Practical's for the Introduction to Python Workshop

jrc_programming_python_practicals

Display many small videos in a grid

video_grid

Zstandard Compression for N5

n5-zstandard

Containerized image processing tools for JACS

jacs-tools

ImageJ Macro

neuronbridge-aligners

Containerized Brain/VNC aligners for NeuronBridge

ImageJ Macro

n5-tools-dask

Dask-based utilities to process N5 images

Inspector for NGFF-style containers supported by the N5 API (N5, HDF5, OME-Zarr)

n5-inspector

Utilities for MolBio MERSCOPE data transfer and processing

merscope-utilities

Semantic search for Janelia resources using GPT models

gpt-semantic-search

jproxy

S3 Proxy

Tests of bundling Python scripts and dependencies into stand-alone executables.

python-dist-demo