Explore @JaneliaSciComp Open Source projects

Howard Hughes Medical Institute (@JaneliaSciComp)

JaneliaSciComp

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Python
25.5 %

Java
12.8 %

JavaScript
10.6 %

MATLAB
9.6 %

C++
6.4 %

Nextflow 6.4 %

Julia
6.4 %

Jupyter Notebook
5.3 %

ImageJ Macro 3.2 %

HTML
2.1 %

Go
2.1 %

Rust
1.1 %

LabVIEW 1.1 %

C#
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Perl
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IGOR Pro 1.1 %

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Location 🇺🇸 United States
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ImageJ Macro 2

Nextflow 7

IGOR Pro 8

LabVIEW 111

Julia
127

XSLT 163

MATLAB
236

Astro 592

Jupyter Notebook
1,429

Groovy
1,641

Java
3,267

C++
3,791

Perl
3,994

Rust
6,060

C#
6,679

Python
6,966

HTML
7,692

Go
8,622

bigstream

Tools for distributed alignment of massive images

Jupyter Notebook

NIDAQ.jl

National Instruments Data Acquisition Interface

JRCLUST

multifish

EASI-FISH analysis pipeline for spatial transcriptomics

Jupyter Notebook

xarray-multiscale

scalable multiscale image pyramids in python

workstation

Janelia Workstation

SongExplorer

deep learning for acoustic signals

SharkViewer

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

pydantic-ome-ngff

Pydantic models for OME-NGFF

osgpyplusplus

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

VVDViewer

3D/4D volumetric rendering of microscopy data

BigStitcher-Spark

Running compute-intense parts of BigStitcher distributed

Wavesurfer

A Matlab application for electrophysiology data analysis

Morton.jl

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

SymmetricFormats.jl

efficient storage for symmetric matrices

nextflow-spark

awesome-janelia-software

A curated list of awesome Janelia software

exllsm-circuit-reconstruction

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

janelia-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 Genotyping

web-vol-viewer

Direct volume rendering with WebGL 2.

Muse

Code for localization of mouse ultrasonic vocalizations using a microphone array

JaneliaDataStandards

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

hortacloud

HortaCloud - 3D annotation platform for large microscopy data

UInt12Arrays.jl

Julia package for supporting arrays of 12-bit integers

Neuroptikon

PyWaveSurfer

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

jacs-cm

JACS Configuration Management

blender-spherical-video

Scripts for Blender to render 360-degree spherical videos.

zarrcade

Create web-based OME-Zarr galleries

Jupyter Notebook

ColorMIP_Mask_Search

ColorMIP_Mask_Search plugin for Fiji

mipav

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

KLEIO-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 environments”

keller-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 search

FlyoVeR

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.

figleaf

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

burst-compute

Burst compute framework for AWS

EM_recon_pipeline

Pipeline scripts and tools for reconstructing Electron Microscopy volumes.

x2s3

BatchedBLAS.jl

batch what Nvidia does not

blender-physics

Scripts to use Blender for physical simulations in python

omnivore

record synchronized audio and video

tmt

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

aitch

local scheduler for heterogenous jobs

java-lsf

Java API to IBM Platform LSF

multiscale-metadata

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

Lightsheet-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-data

KLEIO-Python-SDK

hortacloud-importer

a tiff-to-octree converter for dask

tempo

Media browsing, analysis and annotation

JaneliaGatherMap

Ax

Acoustic Segmenter

G4_Display_Tools

Collection of tools for the G4 LED arena displays.

SAM_service

Web service which generates Segment Anything models

dlc-trainer

A service that trains DeepLabCut models

jrc_intro_programming

Introduction to Python Programming @ Janelia Research Campus

Jupyter Notebook

ShroffCelegansModels.jl

jeiss_fibsem_labview_control

neuronbridge-services

AWS Services for NeuronBridge

PointMatchExplorer

Point Match Explorer for FlyTEM

TileAlignment

Alignment of the overlapping TEM images of the brain

hortacloud-website

Documentation website for HortaCloud

nf-demos

Nextflow Demo Pipelines for Image Processing

ray-janelia

Run Python Ray on the Janelia cluster

2020AprilGitCourse

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

peeling

image_processing_pipeline

Interface to configure pipeline jobs for LightSheet

nf-rsfish

Nextflow wrapper for RS-FISH-Spark

n5-anndata

Convenience functions for reading and writing AnnData files

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 flavors

jacs-model

JACS Domain Model and DAOs

nextflow-dask

TransformationBDV

BDV with transformation feature

tpt

A tentative Python toolbox

lightsheetrecon

janelia-jhdf5

SciJava JHDF5 from Janelia

entrypoints

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

Kafka_examples

Example producer/consumer programs for Kafka

jrc_programming_python_practicals

Practical's for the Introduction to Python Workshop

Jupyter Notebook

video_grid

Display many small videos in a grid

n5-zstandard

Zstandard Compression for N5

jacs-tools

Containerized image processing tools for JACS

neuronbridge-aligners

Containerized Brain/VNC aligners for NeuronBridge

n5-tools-dask

Dask-based utilities to process N5 images

n5-inspector

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

nf-omezarr

Nextflow pipeline for converting images to OME-Zarr using bioformats2raw

merscope-utilities

Utilities for MolBio MERSCOPE data transfer and processing

gpt-semantic-search

Semantic search for Janelia resources using GPT models

ossi-website

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

python-dist-demo

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