%To quantify the total number of Zombie Red pixels

%Input the directory and name of the image files
fileDirectory = ;					
imageZRName = ;

%Input the number of samples
numberOfSample = ;

%Input the region of interest for Zombie Red
startDepthZR = ;
endDepthZR = ;
startTransverseZR = ;
endTransverseZR = ;

%Input the threshold for Zombie Red selection
tValueZR = ;	

%Initialize the variables
imageZRSelectedT(1:endDepthZR-startDepthZR+1,1:endTransverseZR-startTransverseZR+1) = 0;
resultZR(1:numberOfSample) = 0;

%Go through each image sample
for i = 1:numberOfSample

    %load the images
    imageZR = imread(strcat(fileDirectory,imageZRName,int2str(i),'.tif'));

    %Select the region of interest for Zombie Red
    imageZRSelected = imageZR(startDepthZR:endDepthZR,startTransverseZR:endTransverseZR);

    %threshold for Zombie Red selection
    imageZRSelectedT((imageZRSelected>tValueZR)) = 1;
    
    %Show the Zombie Red pixels with an image
    figure(1)
    imshow(imageZRSelectedT,[]);

    %Calculate the total number of Zombie Red pixels
    resultZR(i) = sum(sum(imageZRSelectedT));

end