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/bigstream
Tools for distributed alignment of massive images
JaneliaSciComp/multifish
EASI-FISH analysis pipeline for spatial transcriptomics
JaneliaSciComp/workstation
Janelia Workstation
JaneliaSciComp/SongExplorer
deep learning for acoustic signals
JaneliaSciComp/pydantic-ome-ngff
Pydantic models for OME-NGFF
JaneliaSciComp/JaneliaDataStandards
A pilot experiment to dissminate information about Janelia's biomaging data formats.
JaneliaSciComp/PyWaveSurfer
PyWaveSurfer is a Python package for reading WaveSurfer data files in Python.
JaneliaSciComp/jacs-cm
JACS Configuration Management
JaneliaSciComp/xarray-ome-ngff
Integration between xarray and the ome-ngff data model.
JaneliaSciComp/mipav
MIPAV (Medical Image Processing, Analysis, and Visualization), mirrored from https://citdcbmipav.cit.nih.gov/repos-pub/mipav/
JaneliaSciComp/tmt
A toolbox of Matlab functions useful for data analysis, especially of electrophysiology data.
JaneliaSciComp/G4_Display_Tools
Collection of tools for the G4 LED arena displays.
JaneliaSciComp/colormipsearch
Distributed Color Depth MIP Search
JaneliaSciComp/EM_recon_pipeline
Pipeline scripts and tools for reconstructing Electron Microscopy volumes.
JaneliaSciComp/gpt-semantic-search
Semantic search for Janelia resources using GPT models
JaneliaSciComp/jproxy
S3 Proxy
JaneliaSciComp/neuronbridge-aligners
Containerized Brain/VNC aligners for NeuronBridge
JaneliaSciComp/neuronbridge-precompute
Utilities for indexing and transferring of NeuronBridge-related files
JaneliaSciComp/ossi-website
Website showcasing Janelia Open Science Software Intiative (OSSI) supported software projects and other software developed at Janelia.
JaneliaSciComp/conda-shell
A tool for launching a conda environment in a subshell
JaneliaSciComp/containers
Containers for workflow plugins
JaneliaSciComp/dis-utilities
Utilities for Data and Information Services
JaneliaSciComp/doi_common
Library of common DOI-related functions for Python
JaneliaSciComp/easifish
JaneliaSciComp/jrc_common
Library of common utility functions for Python
JaneliaSciComp/nextflow-modules
Nextflow modules for use with nf-core tooling
JaneliaSciComp/s3-proxy
Reverse Proxy for S3-like file systems
JaneliaSciComp/stitching-spark
Reconstruct big images from overlapping tiled images on a Spark cluster.
JaneliaSciComp/webstation-fetch
Wrapper around isomorphic-fetch to add custom headers to each request
JaneliaSciComp/zarrcade