nunofernandes-plight / cnmf_e

Constrained Nonnegative Matrix Factorization for microEndoscopic data

CNMF_E

Constrained Nonnegative Matrix Factorization for microEndoscopic data

Download

OPTION 1: download the package using this LINK

OPTION 2: (recommended) clone the git repository https://github.com/zhoupc/CNMF_E.git. In this way, you are able to get the latest updates of the package within 1-line command or 1-button click.

Installation

Run cnmfe_setup.m to add CNMF-E package to the search path of MATLAB

>> cnmfe_setup

CNMF-E requires CVX to denoise the extracted calcium traces. CNMF-E will automatically downloaded it and add it to the searching path.

Example

The best way to get started is running a demo script for analyzing an example data.

>> run demos/demo_endoscope.m

Questions

You can ask questions by sending emails to [email protected] or joining our slack channel for discussions.

Reference

Please cite this paper when you use CNMF-E in your research. Thanks!

Zhou, P., Resendez, S.L., Rodriguez-Romaguera, J., Jimenez, J.C, Neufeld, S.Q., Stuber, G.D., Hen, R., Kheirbek, M.A., Sabatini, B.L., Kass, R.E., Paninski, L. (2016). Efficient and accurate extraction of in vivo calcium signals from microendoscopic video data. arXiv Prepr, arXiv1605.07266.

License

Copyright 2016 Pengcheng Zhou

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.