%% Cell count addition to intensity quantification script

% Author: Jordan Rolsma - University of California, Riverside

%Features: 

    %Counts cell nuclei within phalloidin borders (debris and artifacts are
    %filtered out in the main script).

    %Outputs individual tilescan figures with traced nuclei and cell count
    %printed on each one.

    %Note: To use, call this script or paste it directly into the intensity
    %quantification script below the 'plot trace of nuclei' for loop.

    %If you wish to save the cell count data, include 'nuccount' as an
    %input in the line below:

    %save(sprintf('%s\\%s\\%s_data.mat',outdir1,outdir2,IM_FILE(1:end-4)),'Sname','intDataNuc','intDataCyt','intDataRat','nuccount')


%% Code

     %Plot trace of nuclei
            for f = 1:length(B)
                boundary = B{f};
                plot(boundary(:,2), boundary(:,1), 'm', 'LineWidth', 1)

                nuccount = size(centroid(:,1));

              if nuccount > 0
                  nuccount{g} = nuccount;
                  text(700,-50,['Nuclei count:' num2str(nuccount{g})],'color','r','FontSize',14,'FontWeight','bold'); 
              else 
                 continue 
              end