realignementScript.m

%% Paramters
%input file
inFileGren = 'D:\data\BelenTestData\Out\complete_g.tif';
inFileRed = 'D:\data\BelenTestData\Out\complete_g.tif';

%oiutput file
outFileGreen = 'D:\data\BelenTestData\Out\complete_g_Grealigned.tif';
outFileRed = 'D:\data\BelenTestData\Out\complete_g_Rrealigned.tif';

%Apply Gaussian Filter before correction?
bGaussian = 0;

%reference channels
referenceChannel = 1; %1: red, 0: green
numShiftCorrections = 1;

nSubIm = 200;%number of subImages for med align
numImages = 50; %number of images that will be meaned for global shift correction
%% Load data and perform correction
data_r = loadtiff(inFileRed);
data_g = loadtiff(inFileGren);

for j = 1:numShiftCorrections
    if referenceChannel
        referenceChannelData = data_r;
    else
        referenceChannelData = data_g;
    end
    
    if bGaussian
        for f=1:size(referenceChannelData,3)
            referenceChannelData(:,:,f) = imgaussfilt(referenceChannelData(:,:,f),2);
        end
    end
    
    %Med Align
    [rs, cs] = medAlign(referenceChannelData, nSubIm, 50, -inf);
    %shift red and green channel
    %waitbar(j/numShiftCorrections, wb, 'Performing Med Align..');
    for i = 1:size(data_g,3)
        data_r(:,:,i) = circshift(data_r(:,:,i),[rs(i),cs(i)]);
        data_g(:,:,i) = circshift(data_g(:,:,i),[rs(i),cs(i)]);
    end
end

%% Exort Data

saveastiff(data_r, outFileRed);
saveastiff(data_g, outFileGreen);