Discover JaneliaSciComp/mipav 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

figleaf

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

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

Website showcasing Janelia Open Science Software Intiative (OSSI) supported software projects and other software developed at Janelia.

ossi-website

Astro

jproxy

S3 Proxy

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

python-dist-demo