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 Lim et al., 2012, 2014). 

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

To use this package: 
1. Unzip data files and ensure all Matlab functions are in the same directory as the NetworkAnalysis_VSD.m
2. Open NetworkAnalysis_VSD.m with Matlab
3. In NetworkAnalysis_VSD.m, enter the folder name where the data is stored (line 5)
4. Execute code.

See corresponding articles: 
Lim et al.(2012). In vivo Large-Scale Cortical Mapping Using Channelrhodopsin-2 Stimulation in Transgenic Mice Reveals Asymmetric and Reciprocal Relationships between Cortical Areas. Front Neural Circuits 6:11.
Lim et al.(2014). Optogenetic mapping after stroke reveals network-wide scaling of functional connections and heterogeneous recovery of the peri-infarct. J Neurosci 34:16455-16466.

See also: 
Brain connectivity toolbox: https://sites.google.com/site/bctnet/ 
Rubinov and Sporns (2010). Complex network measures of brain connectivity: uses and interpretations. Neuroimage 52:1059-1069.





Diana Lim and Jeffrey LeDue, University of British Columbia, 2015.