intern

intern

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.

Getting Started

To quickly get started with intern, check out the wiki: https://github.com/jhuapl-boss/intern/wiki

Documentation

Full detailed documentation can be found here: https://jhuapl-boss.github.io/intern/

Installation

• 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

• Using virtualenvwrapper:

mkvirtualenv intern

• (Preferred) Install via pypi

pip install intern

• Install via git

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.

Optional Dependencies

To install depedencies required to use the cloud-volume remote, run the command:

pip install intern[cloudvolume]

Contributing

Please submit bug reports, or get in touch using GitHub Issues.

Citation

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}
}

The Boss Legal Notes

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:

1. Redistributions of source code or binary forms must adhere to the terms and conditions of any applicable software licenses.
2. End-user documentation or notices, whether included as part of a redistribution or disseminated as part of a legal or scientific disclosure (e.g. publication) or advertisement, must include the following acknowledgement: The Boss software system was designed and developed by the Johns Hopkins University Applied Physics Laboratory (JHU/APL).
3. The names "The Boss", "JHU/APL", "Johns Hopkins University", "Applied Physics Laboratory", "MICrONS", or "IARPA" must not be used to endorse or promote products derived from this software without prior written permission. For written permission, please contact [e-mail].
4. This source code and library is distributed in the hope that it will be useful, but is provided without any warranty of any kind.