lowon_fxn.m~

%% lowon_fxn.m

% Alistair Boettiger                                 Date Begun: 03/17/2010
% Levine Lab                      This Version Functional Since: 04/03/2010
%                                                 Last Modified: 04/04/2010

%% Description
% Compute relative varabililty in total intensity between nuclei.
% Written for Plot_DotComps family code to analyse shadow data. 
%
%
%% Updates
% updated 04/03/2010 to normalize intensities before trying to compare
% relative varibility in total transcript counts


%% Source Code

function [lowon, corr_var] = lowon_fxn(H,handles,nin2,ptr_nucin2,emb)
%lowon = lowon_fxn(H,handles,all_nucs,pts2,nin2,Cell_bnd)
 
    cell_int = H; 
       Nnucs = max(H(:));
        mu_I = zeros(Nnucs,1); 
       % mu_N = zeros(Nnucs,1); sig_I = zeros(Nnucs,1);
        reg_data = regionprops(H,'PixelIdxList');
            for i=1:Nnucs; 
                pixes = reg_data(i).PixelIdxList;      
                mu_I(i) = median(handles.Im1(pixes));
              %  mu_N(i) = median(handles.In(pixes));
              %  sig_I(i) = std(double(handles.Im1(pixes));             
                cell_int(pixes) = mu_I(i);
            end
 % lowon = std(mu_I(nin2))/mean(mu_I(nin2));
      mvar = mu_I(nin2)-min(mu_I(nin2));
      mvar = mvar/max(mvar); 
    
      cvar =    mu_I-min(mu_I);
      cvar = cvar/max(cvar); 
      
        lowon = std(mvar)./mean(mvar);    

N = sum(nin2);
C = handles.conn_map; 
eta = zeros(1,N); 

      for i=1:N; % loop through nucs in region
          nuc = ptr_nucin2(i); 
          neibs = find(C(nuc,:)>0);  
%        %   figure(1); clf; M = ismember(H,neibs); imshow(M);
          sig = std(cvar(neibs));
          mu = mean(cvar(neibs));
          eta(i) = sig/mu; 
      end

%             
            
       corr_var = mean(eta);       
 
       
     %  %   Plotting 
%           cell_int = uint8( 255*cell_int./max(cell_int(:))  );     
%             figure(3); clf; 
%        [h,w] = size(H);
%                 Io = uint8(zeros(h,w,3));
%                 Io(:,:,1) = imadd(uint8(cell_int),handles.Im1); 
%                 Io(:,:,2) =  handles.Im2 ;% imadd(handles.Im2,uint8(255*L2.*Cell_bnd));
%                 Io(:,:,3) =   handles.In; 
%                clf; imshow(Io); 
%                title([emb, '   eta = ' num2str(lowon,2), '  corr var=',...
%                    num2str(corr_var,2),'   mu =',num2str(mean(mu_I(nin2)),2)],...
%                    'FontSize',16);        
%              figure(1); clf; hist(mu_I(nin2));
%                pause(1); 
% % %