This package of sample data and MATLAB codes will process, filter, and average raw voltage sensitive dye images, generate a comprehensive connectivity matrix and a network diagram, as seen in:
Requirements:
MATLAB (with Bioinformatics Toolbox and Brain Connectivity Toolbox)
Inputs:
sample data; MATLAB functions; Mask.tif (as included in .zip file)
Outputs:
dF/F0(%) VSD connectivity matrix; Figure of network properties as a function of threshold levels; Network diagram
Lim DH, Mohajerani MH, LeDue J, Boyd J, Chen S, Murphy TH. In vivo large-scale cortical mapping using channelrhodopsin-2 stimulation in transgenic mice reveals asymmetric and reciprocal relationships between cortical areas. Front Neural Circuits. 2012;6:11. doi:10.3389/fncir.2012.00011
Lim DH, LeDue JM, Murphy TH. Network analysis of mesoscale optical recordings to assess regional, functional connectivity. Neurophotonics. 2015;2(4):041405. doi:10.1117/1.nph.2.4.041405