llerussell / ntc_cnmf Goto Github PK

The code implements a method (constrained non-negative matrix factorization, CNMF) for simultaneous source extraction from large scale calcium imaging movies. The algorithm is presented in more detail here: http://arxiv.org/abs/1409.2903

The CNMF code is written by Eftychios A. Pnevmatikakis and Liam Paninski, with inputs from Weijian Yang and Darcy S. Peterka. They are also stored in https://github.com/epnev/ca_source_extraction.

The demo script are written by Eftychios A. Pnevmatikakis, Liam Paninski, Weijian Yang and Darcy S. Peterka, 2015.

Please first download and install cvx matlab package from http://cvxr.com/cvx/

Use "demo_script2.m" to run the CNMF algorithm. "demoMovie.tif" is a calcium image movie for code demo.

Use "dataProcessing.m" to extract results after "demo_script2.m" is ran.

"dataProcessing.m" can save a .mat file which contains the CNMF parameters and the results. Use "file_dataProcessing.m" to reload the results from the saved .mat file.