potcelltraces.m

 % plot cell tracesfor the specific outfile
 
 function potcelltraces(outfile,trajmin)
 % get time dependent data for a given .mat file ( plot each colony in
 % different figure)
 %colSZ = 3;
 %p2 = (resptime+jumptime)*delta_t/60;
 %coloniestoanalyze = 3;
 %cmap = summer;
 C = {'r','b','g','m','b','c','g'};
 %outfile = ('16_40X_tbsht1Z.mat');%3Dsegm_febdata    3D_20hr_test_xyz   % 7 ,16, 15, 18 29 26 31  reanalyze
 load(outfile,'colonies','peaks');
 % tps = length(peaks);
 numcol = size(colonies,2); % how many colonies were grouped within the frame
 traces = cell(1,numcol);
 for j = 1:numcol
     traces{j} = colonies(j).NucSmadRatio(:);
     %colSZ = colonies(j).numOfCells(timecolSZ);
     traces{j}((traces{j} == 0)) = nan;
     for h = 1:size(traces{j},2)
         if length(traces{j}(isnan(traces{j}(:,h))==0))>trajmin
             figure(j), plot(traces{j}(:,h),'-*','color',C{j});hold on% cmap(j,:) 'r' traces
             q = 1;
             ylim([0 2]);
             ylabel('mean Nuc/Cyto smad4  ');
             xlabel('frames');
         end
     end
 end
 end