Howard Hughes Medical Institute
GitHub organization maintained by Scientific Computing Software at HHMI's Janelia Research Campus for use by HHMI staff and external collaborators.
19700 Helix Drive, Ashburn, VA 20147
Pinned Repositories
bigstream
Tools for distributed alignment of massive images
JRCLUST
JRCLUST
multifish
EASI-FISH analysis pipeline for spatial transcriptomics
NIDAQ.jl
National Instruments Data Acquisition Interface
osgpyplusplus
Python bindings for OpenSceneGraph 3D graphics API, created using Boost.Python and Py++
SharkViewer
SharkViewer is a web-based viewer for SWC neuron files. It is written entirely in JavaScript using Three.js.
SongExplorer
deep learning for acoustic signals
Wavesurfer
A Matlab application for electrophysiology data analysis
workstation
Janelia Workstation
xarray-multiscale
scalable multiscale image pyramids in python
Howard Hughes Medical Institute's Repositories
JaneliaSciComp/SongExplorer
deep learning for acoustic signals
JaneliaSciComp/neuronbridge
EM/LM neuron search
JaneliaSciComp/aitch
local scheduler for heterogenous jobs
JaneliaSciComp/tmt
A toolbox of Matlab functions useful for data analysis, especially of electrophysiology data.
JaneliaSciComp/hortacloud-website
Documentation website for HortaCloud
JaneliaSciComp/neuronbridge-services
AWS Services for NeuronBridge
JaneliaSciComp/nf-rsfish
Nextflow wrapper for RS-FISH-Spark
JaneliaSciComp/gpt-semantic-search
Semantic search for Janelia resources using GPT models
JaneliaSciComp/ImagingEcosystem
The Imaging Ecosystem (well, parts of it, anyway).
JaneliaSciComp/jacs-model
JACS Domain Model and DAOs
JaneliaSciComp/jacs-tools
Containerized image processing tools for JACS
JaneliaSciComp/Kafka_examples
Example producer/consumer programs for Kafka
JaneliaSciComp/freight
Python tools for moving stuff around
JaneliaSciComp/IJava
A Jupyter kernel for executing Java code.
JaneliaSciComp/jacs-tools-docker
Tools for JACS, containerized with Docker
JaneliaSciComp/jPubTrack
Miscellaneous scripts for managing Janelia's publication data.
JaneliaSciComp/jrc_common
Library of common utility functions for Python
JaneliaSciComp/n5-anndata
Convenience functions for reading and writing AnnData files
JaneliaSciComp/neuronbridge-data
Versioned NeuronBridge data files deployed to S3 buckets
JaneliaSciComp/neuronbridge-python
Python API for NeuronBridge
JaneliaSciComp/nextflow-bigstream
BigStream Nextflow Workflow
JaneliaSciComp/nf-n5-spark
Nextflow wrapper for saalfeldlab/n5-spark
JaneliaSciComp/nf-omezarr
Nextflow pipeline for converting images to OME-Zarr
JaneliaSciComp/ngffbrowse
JaneliaSciComp/nnmf
Non-negative matrix factorization of fluorescent time series
JaneliaSciComp/pysolo-tools
JaneliaSciComp/stitching-spark
Reconstruct big images from overlapping tiled images on a Spark cluster.
JaneliaSciComp/test-datasets
This contains test data for the BioImageTools nextflow modules
JaneliaSciComp/transfero
Python scripts for transferring data from rig computers
JaneliaSciComp/Zebrafish_96well_segmentation_mesure_FPC
Zebrafish 2D auto-segmentation & FPC auto-mesurement