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Awesome

An open API service indexing awesome lists of open source software.

Projects in Awesome Lists by JaneliaSciComp

A curated list of projects in awesome lists by JaneliaSciComp .

https://github.com/janeliascicomp/bigstream

Tools for distributed alignment of massive images

Last synced: 04 Apr 2025

https://github.com/JaneliaSciComp/bigstream

Tools for distributed alignment of massive images

Last synced: 16 Apr 2025

https://github.com/janeliascicomp/nidaq.jl

National Instruments Data Acquisition Interface

Last synced: 21 Feb 2025

https://github.com/janeliascicomp/multifish

EASI-FISH analysis pipeline for spatial transcriptomics

easi-fish ibm-platform-lsf nextflow pipeline

Last synced: 15 Apr 2025

https://github.com/JaneliaSciComp/multifish

EASI-FISH analysis pipeline for spatial transcriptomics

easi-fish ibm-platform-lsf nextflow pipeline

Last synced: 16 Apr 2025

https://github.com/janeliascicomp/xarray-multiscale

scalable multiscale image pyramids in python

Last synced: 19 Apr 2025

https://github.com/JaneliaSciComp/xarray-multiscale

scalable multiscale image pyramids in python

Last synced: 16 Apr 2025

https://github.com/janeliascicomp/bigstitcher-spark

Running compute-intense parts of BigStitcher distributed

Last synced: 19 Apr 2025

https://github.com/janeliascicomp/songexplorer

deep learning for acoustic signals

Last synced: 19 Apr 2025

https://github.com/janeliascicomp/sharkviewer

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

Last synced: 16 Jul 2025

https://github.com/janeliascicomp/pydantic-ome-ngff

Pydantic models for OME-NGFF

Last synced: 07 Sep 2025

https://github.com/janeliascicomp/morton.jl

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

Last synced: 27 Aug 2025

https://github.com/janeliascicomp/vvdviewer

3D/4D volumetric rendering of microscopy data

microscopy neuroscience rendering vvd-viewer

Last synced: 24 Oct 2025

https://github.com/JaneliaSciComp/SongExplorer

deep learning for acoustic signals

Last synced: 16 Apr 2025

https://github.com/janeliascicomp/wavesurfer

A Matlab application for electrophysiology data analysis

Last synced: 19 Apr 2025

https://github.com/janeliascicomp/osgpyplusplus

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

Last synced: 19 Apr 2025

https://github.com/JaneliaSciComp/VVDViewer

3D/4D volumetric rendering of microscopy data

microscopy neuroscience rendering vvd-viewer

Last synced: 16 Apr 2025

https://github.com/janeliascicomp/janelia-unity-toolkit

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

Last synced: 19 Apr 2025

https://github.com/janeliascicomp/zarrcade

Create web-based OME-Zarr galleries

microscopy-images ome-zarr webapp

Last synced: 19 Apr 2025

https://github.com/janeliascicomp/symmetricformats.jl

efficient storage for symmetric matrices

Last synced: 21 Feb 2025

https://github.com/janeliascicomp/exllsm-circuit-reconstruction

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

image-processing lightsheet machine-learning microscopy neuroscience nextflow-pipelines pipeline segmentation

Last synced: 25 Jan 2026

https://github.com/JaneliaSciComp/janelia-unity-toolkit

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

Last synced: 16 Apr 2025

https://github.com/JaneliaSciComp/exllsm-circuit-reconstruction

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

image-processing lightsheet machine-learning microscopy neuroscience nextflow-pipelines pipeline segmentation

Last synced: 16 Apr 2025

https://github.com/janeliascicomp/janeliadatastandards

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

Last synced: 11 Feb 2026

https://github.com/janeliascicomp/msg

Multiplexed Shotgun Genotyping

Last synced: 15 Jun 2025

https://github.com/JaneliaSciComp/web-vol-viewer

Direct volume rendering with WebGL 2.

Last synced: 16 Apr 2025

https://github.com/janeliascicomp/three-orbit-unlimited-controls

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

Last synced: 19 Apr 2025

https://github.com/janeliascicomp/web-vol-viewer

Direct volume rendering with WebGL 2.

Last synced: 19 Apr 2025

https://github.com/janeliascicomp/hortacloud

HortaCloud - 3D annotation platform for large microscopy data

annotation-tool aws janelia neurons neuroscience scientific-computing

Last synced: 19 Apr 2025

https://github.com/janeliascicomp/muse

Code for localization of mouse ultrasonic vocalizations using a microphone array

Last synced: 21 Feb 2025

https://github.com/janeliascicomp/pywavesurfer

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

Last synced: 19 Apr 2025

https://github.com/janeliascicomp/uint12arrays.jl

Julia package for supporting arrays of 12-bit integers

Last synced: 21 Feb 2025

https://github.com/janeliascicomp/blender-spherical-video

Scripts for Blender to render 360-degree spherical videos.

Last synced: 13 Oct 2025

https://github.com/JaneliaSciComp/blender-spherical-video

Scripts for Blender to render 360-degree spherical videos.

Last synced: 16 Apr 2025

https://github.com/janeliascicomp/neuroptikon

Neuroptikon

Last synced: 19 Apr 2025

https://github.com/JaneliaSciComp/UInt12Arrays.jl

Julia package for supporting arrays of 12-bit integers

Last synced: 16 Apr 2025

https://github.com/janeliascicomp/x2s3

S3 Proxy Service

s3 s3-bucket s3-storage

Last synced: 11 Dec 2025

https://github.com/janeliascicomp/xarray-ome-ngff

Integration between xarray and the ome-ngff data model.

Last synced: 19 Apr 2025

https://github.com/janeliascicomp/colormip_mask_search

ColorMIP_Mask_Search plugin for Fiji

Last synced: 06 Feb 2026

https://github.com/janeliascicomp/kleio-java-sdk

Versioned Storage Java SDK: Block based versioned data storage.

datastructures java kleio version-control

Last synced: 05 Oct 2025

https://github.com/janeliascicomp/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.

Last synced: 05 Sep 2025

https://github.com/janeliascicomp/cohenbolstadlee_elife2017

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

Last synced: 19 Apr 2025

https://github.com/janeliascicomp/maru

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

computational-plugins container containerization docker hpc scientific-computing

Last synced: 19 Apr 2025

https://github.com/JaneliaSciComp/maru

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

computational-plugins container containerization docker hpc scientific-computing

Last synced: 16 Apr 2025

https://github.com/janeliascicomp/mipav

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

Last synced: 19 Apr 2025

https://github.com/janeliascicomp/batchedblas.jl

batch what Nvidia does not

Last synced: 09 Oct 2025

https://github.com/janeliascicomp/figleaf

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

Last synced: 27 Oct 2025

https://github.com/janeliascicomp/datapro

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

Last synced: 15 Sep 2025

https://github.com/janeliascicomp/burst-compute

Burst compute framework for AWS

aws-lambda burst-parallel compute-engine hpc

Last synced: 19 Apr 2025

https://github.com/JaneliaSciComp/burst-compute

Burst compute framework for AWS

aws-lambda burst-parallel compute-engine hpc

Last synced: 16 Apr 2025

https://github.com/JaneliaSciComp/ColorMIP_Mask_Search

ColorMIP_Mask_Search plugin for Fiji

Last synced: 16 Apr 2025

https://github.com/janeliascicomp/tmt

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

Last synced: 19 Apr 2025

https://github.com/janeliascicomp/em_recon_pipeline

Pipeline scripts and tools for reconstructing Electron Microscopy volumes.

Last synced: 19 Apr 2025

https://github.com/janeliascicomp/java-lsf

Java API to IBM Platform LSF

cluster hpc janelia lsf

Last synced: 14 Jul 2025

https://github.com/janeliascicomp/multiscale-metadata

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

Last synced: 05 Feb 2026

https://github.com/janeliascicomp/aitch

local scheduler for heterogenous jobs

Last synced: 06 Aug 2025

https://github.com/janeliascicomp/omnivore

record synchronized audio and video

Last synced: 21 Feb 2025

https://github.com/janeliascicomp/blender-physics

Scripts to use Blender for physical simulations in python

Last synced: 21 Feb 2025

https://github.com/janeliascicomp/lightsheet-processing-pipeline

Pipeline from Philipp Keller (kellerp@janelia.hhmi.org) 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

Last synced: 21 Feb 2025

https://github.com/JaneliaSciComp/spark-janelia

scripts for using spark on janelia's cluster

Last synced: 16 Apr 2025

https://github.com/JaneliaSciComp/java-lsf

Java API to IBM Platform LSF

cluster hpc janelia lsf

Last synced: 16 Apr 2025

https://github.com/janeliascicomp/ray-janelia

Run Python Ray on the Janelia cluster

cluster compute-clusters distributed-computing janelia ray

Last synced: 08 Feb 2026

https://github.com/janeliascicomp/nf-rsfish

Nextflow wrapper for RS-FISH-Spark

Last synced: 27 Jan 2026

https://github.com/janeliascicomp/g4_display_tools

Collection of tools for the G4 LED arena displays.

Last synced: 19 Apr 2025

https://github.com/janeliascicomp/hortacloud-website

Documentation website for HortaCloud

hortacloud janelia neuroscience

Last synced: 21 Feb 2025

https://github.com/janeliascicomp/ax

Acoustic Segmenter

Last synced: 25 Oct 2025

https://github.com/janeliascicomp/image_processing_pipeline

Interface to configure pipeline jobs for LightSheet

Last synced: 21 Feb 2025

https://github.com/janeliascicomp/web-h5j-loader

Lets browser apps load H5J data files.

Last synced: 30 Oct 2025

https://github.com/janeliascicomp/dlc-trainer

A service that trains DeepLabCut models

Last synced: 25 Aug 2025

https://github.com/janeliascicomp/jrc_intro_programming

Introduction to Python Programming @ Janelia Research Campus

Last synced: 26 Sep 2025

https://github.com/janeliascicomp/tempo

Media browsing, analysis and annotation

Last synced: 21 Feb 2025

https://github.com/janeliascicomp/sam_service

Web service which generates Segment Anything models

Last synced: 17 Nov 2025

https://github.com/janeliascicomp/neuronbridge-services

AWS Services for NeuronBridge

Last synced: 04 Jul 2025

https://github.com/janeliascicomp/pointmatchexplorer

Point Match Explorer for FlyTEM

Last synced: 07 Jul 2025

https://github.com/janeliascicomp/tilealignment

Alignment of the overlapping TEM images of the brain

Last synced: 21 Feb 2025

https://github.com/janeliascicomp/gpt-semantic-search

Semantic search for Janelia resources using GPT models

Last synced: 30 Jun 2025

https://github.com/JaneliaSciComp/ray-janelia

Run Python Ray on the Janelia cluster

cluster compute-clusters distributed-computing janelia ray

Last synced: 16 Apr 2025

https://github.com/janeliascicomp/hortacloud-importer

a tiff-to-octree converter for dask

Last synced: 19 Apr 2025

https://github.com/JaneliaSciComp/G4_Display_Tools

Collection of tools for the G4 LED arena displays.

Last synced: 16 Apr 2025

https://github.com/JaneliaSciComp/web-h5j-loader

Lets browser apps load H5J data files.

Last synced: 16 Apr 2025

https://github.com/janeliascicomp/nf-demos

Nextflow Demo Pipelines for Image Processing

image-processing nextflow

Last synced: 27 Jan 2026

https://github.com/janeliascicomp/2020aprilgitcourse

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

Last synced: 21 Feb 2025

https://github.com/JaneliaSciComp/entrypoints

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

docker entrypoint oci

Last synced: 16 Apr 2025

https://github.com/janeliascicomp/funkeannotation

Small tool to annotate images

Last synced: 16 Oct 2025

https://github.com/janeliascicomp/n5-tools-dask

Dask-based utilities to process N5 images

Last synced: 21 Feb 2025