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/web-vol-viewer
Direct volume rendering with WebGL 2.
JaneliaSciComp/burst-compute
Burst compute framework for AWS
JaneliaSciComp/aitch
local scheduler for heterogenous jobs
JaneliaSciComp/java-lsf
Java API to IBM Platform LSF
JaneliaSciComp/hortacloud-website
Documentation website for HortaCloud
JaneliaSciComp/nf-demos
Nextflow Demo Pipelines for Image Processing
JaneliaSciComp/nf-rsfish
Nextflow wrapper for RS-FISH-Spark
JaneliaSciComp/ImagingEcosystem
The Imaging Ecosystem (well, parts of it, anyway).
JaneliaSciComp/jacs-tools
Containerized image processing tools for JACS
JaneliaSciComp/Kafka_examples
Example producer/consumer programs for Kafka
JaneliaSciComp/merscope-utilities
Utilities for MolBio MERSCOPE data transfer and processing
JaneliaSciComp/n5-tools-dask
Dask-based utilities to process N5 images
JaneliaSciComp/n5-zstandard
Zstandard Compression for N5
JaneliaSciComp/web-h5j-loader
Lets browser apps load H5J data files.
JaneliaSciComp/EM_MIP_search
JaneliaSciComp/easi-fish-np-backend
Backend processing for EASI-FISH-NP
JaneliaSciComp/elk-utilities
Utilities for ELK stack configuration, maintenance, and use
JaneliaSciComp/freight
Python tools for moving stuff around
JaneliaSciComp/Groundswell
A Matlab application for browsing and analysis of electrophysiology data.
JaneliaSciComp/n5-anndata
Convenience functions for reading and writing AnnData files
JaneliaSciComp/neuronbridge-vol-viewer
Website incorporating @janelia/web-vol-viewer for direct volume rendering of neuronbridge matches
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/nnmf
Non-negative matrix factorization of fluorescent time series
JaneliaSciComp/PEELing_web
JaneliaSciComp/pppm-website
PatchPerPix Match website
JaneliaSciComp/pysolo-tools
JaneliaSciComp/test-datasets
This contains test data for the BioImageTools nextflow modules
JaneliaSciComp/tmog
The Janelia Transmogrifier - tmog - supports the collection of meta data associated with files.