MergeStackMPTIFFA488.m

function [ Ind ] = MergeStackMPTIFFA488( fname, first, last )

% This function reads the input TIF image stack 'fname', merge the first
% 'num' number of frames into a new single frame TIF file called 'fname_m.TIF'
% fname must be the full filename of a stack tiff image

sname = strcat(strtok(fname,'.'),'_m.TIF');

info = imfinfo(fname);
img_height = info(1,1).Height;
img_width = info(1,1).Width;

third = round(img_width/3);

% pre-allocate space for image stack
clear('imgstk', 'imgmrg');
imgstk = zeros(img_height, img_width, last-first+1, 'uint16');
imgmrg = zeros(img_height, round(img_width/3), 'uint16');

% load first few frames of the tiff stack, number of frames indicated by
% % num
% for k = 1:num
%     imgstk(:,:,k) = imread(fname, k, 'Info', info);
%     
% end

[imgstk,n] = imread(fname);

for k = first:last
    imgstk(:,:,k+1-first) = imread(fname, k, 'Info', info);
end

% figure
% image(imgstk(:, :, 1),'CDataMapping','scaled')
% colormap(gray)

% create the merged image from the average of the image stack
for i = 1:img_height
    for j = 2*third+1:img_width
        imgmrg(i,j-2*third) = mean(imgstk(i,j,:)); %imgmrg(i,j) = mean(imgstk(i,j,:));
    end
end

% plot the merged image
figure
imshow(imgmrg, [])%,'scaled')
colormap(gray)

imwrite(imgmrg, sname, 'tif');
Ind = j;
end