intern (Integrated Toolkit for Extensible and Reproducible Neuroscience) is a Python 3 module that enables big-data neuroscience. Currently, it provides an interface to common big-data neuroimaging databases such as BossDB, CloudVolume, DVID, and other standard formats.
To quickly get started with intern, check out the wiki: https://github.com/jhuapl-boss/intern/wiki
Full detailed documentation can be found here: https://jhuapl-boss.github.io/intern/
It's always a good idea to use virtualenv to isolate your work from your system Python installation:
Using virtualenv:
virtualenv intern
. intern/bin/activate
mkvirtualenv intern
pip install intern
Clone the repository from https://github.com/jhuapl-boss/intern and run
pip install -r requirements.txt
from the repository's location on your
system.
Add <repository location>
to your PYTHONPATH
.
For example, on a *nix system, if intern was cloned to ~/intern:
export PYTHONPATH=$PYTHONPATH:~/intern
For Python 2 support, you will need to install intern v0.10.0 or earlier.
To install depedencies required to use the cloud-volume remote, run the command:
pip install intern[cloudvolume]
Please submit bug reports, or get in touch using GitHub Issues.
If you find this library useful to your work, please consider citing the following:
https://www.biorxiv.org/content/10.1101/2020.05.15.098707v1
@article{intern,
doi = {10.1101/2020.05.15.098707},
url = {https://www.biorxiv.org/content/10.1101/2020.05.15.098707v1},
year = 2020,
month = {may},
publisher = {BiorXiv},
author = {Matelsky, Jordan K and Rodriguez, Luis and Xenes, Daniel and Gion, Timothy and Hider Jr., Robert and Wester, Brock and Gray-Roncal, William},
title = {{intern: Integrated Toolkit for Extensible and Reproducible Neuroscience}},
journal = {BiorXiv}
}
Use or redistribution of the Boss system in source and/or binary forms, with or without modification, are permitted provided that the following conditions are met: