MTbundling.m

function MTbundling

% Luigi AR localization

% open file manually

        [fileName,dirName] = uigetfile('*.tif','Choose a .tif file');
        I = imread([dirName,fileName]);
        Idapi = imread([dirName,fileName(1:end-7),'Dapi.tif']);
Iar = imread([dirName,fileName(1:end-7),'ARGFP.tif']);
% DoG
    nor=1;%2^16;
I=double(I)/nor;
Iar=double(Iar)/nor;
     Idapi = double(Idapi)/nor;
     
     [cutoffInd4, cutDAPI] = cutFirstHistMode(Idapi,0);
 Idapi2 = Idapi>cutDAPI*2;
  figure,imshow(Idapi,[])
 figure,imshow(Idapi2,[])
   figure,imshow(Iar,[])
%  distance_image = bwdist(~Idapi2);
% 
% figure, imshow(distance_image,[])
% colormap(bone)
% colorbar
 
Id2 = bwmorph(Idapi2,'dilate');
Id7 = bwmorph(Id2,'dilate');
% Id2 = bwmorph(Id3,'dilate');
% Id5 = bwmorph(Id4,'dilate');
% Id6 = bwmorph(Id5,'dilate');
% Id7 = bwmorph(Id6,'dilate');
Idn = Id7 - Idapi2;

    X = bwlabel(Idn);
 
    stats = regionprops(X,'all');  
    
% list = stats(5).PixelIdxList;
% Itest = zeros(size(I,1),size(I,2));
% Itest(list) = I(list);
% figure,imshow(Itest,[])    

Iaux = Idn.*Iar; % read the AR channel
figure,imshow(Iaux,[])    
colormap(jet)
colorbar

hold on

for i = 1: length(stats) % CYTOPLASM
    s(i) = ceil(sum(Iar(stats(i).PixelIdxList))/length(stats(i).PixelIdxList)); % NORMALIZE AR INT PER AREA

 
    text(stats(i).Centroid(1)-5,stats(i).Centroid(2)-5,[num2str(s(i))],'Color','r');

end
%-------------------------------------------------------------
 

    X1 = bwlabel(Idapi2);
 
    stats1 = regionprops(X1,'all');  
    
     

Iaux1 = Idapi2.*Iar; % read the AR channel
figure,imshow(Iaux1,[])    
colormap(jet)
colorbar

hold on

for i = 1: length(stats1) % NUCLEAR
    s1(i) = ceil(sum(Iar(stats1(i).PixelIdxList))/length(stats1(i).PixelIdxList));% NORMALIZE AR INT PER AREA

 
    text(stats1(i).Centroid(1)-5,stats1(i).Centroid(2)-5,[num2str(s1(i))],'Color','r');

end

sa=sort(s);
s1a=sort(s1);

NUC_TO_CYTO_AR = mean(s1a(end-5:end))/mean(sa(end-5:end))