%Calculate Redox Ratio

%Adapted from Quinn Lab

%By: Shelby Bess

%Date: April 4, 2022

% Load images

nadh = imread('06-755-006-Ch3-16bit-Reference.tif');

fad = imread('06-855-006-Ch2-16bit-Reference.tif');

% Load image metadata

nadh_meta = xml2imagedata('06-755-006.xml');

fad_meta = xml2imagedata('06-855-006.xml');

% Get the values necessary for fluorescein normalizing images. These values 

should be loaded appropriately, but are hard coded here.

pockels_755 = [50,62,80,70];

power_755 = [71.3,87.82,110.9,98.3];

pockels_855 = [30,45,60,51];

power_855 = [56.22,85.44,109.8,94.3];

% Normalize images

nadh = 

fluorescein_normalization_master(nadh,nadh_meta.pmtGain.PMT3_Blue_,pockels_75

5(end),'-obj',pockels_755,power_755,nadh_meta.date,'-i');

fad = 

fluorescein_normalization_master(fad,fad_meta.pmtGain.PMT2_Green_,pockels_855(

end),'-obj',pockels_855,power_855,fad_meta.date,'-i');

figure; imagesc((nadh+fad)./2);

title('Average fluorescence intensity'); colormap gray; colorbar;

[orr,avgFluorescenceORR] = calculateRedoxRatio(nadh,fad);

fprintf(['Average fluorescence redox ratio for whole image: 

',num2str(avgFluorescenceORR,4)]);

figure; imagesc(orr);

title('Optical redox ratio'); caxis([0 1]); colormap jet; colorbar;

mask = imread('Mask.tif');

mask=double(mask);

[~,avgFluorescenceORR] = calculateRedoxRatio(nadh,fad,mask);

fprintf(['Average fluorescence redox ratio within ROI: 

',num2str(avgFluorescenceORR,4)]);

figure; imagesc(((nadh+fad)./2).*mask);

title('Masked ROI'); colormap gray

[colorORR,cmap] = createColorORRMap(orr,(fad+nadh)./2);

figure; imagesc(colorORR);

title('Colored ORR image'); colormap(cmap); caxis([0 1]); c = 

colorbar('Ticks',[0 1]);

Error using imread>get_full_filename

File "06-755-006-Ch3-16bit-Reference.tif" does not exist.

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Error in imread (line 372)

 fullname = get_full_filename(filename);

Error in Redox (line 7)

nadh = imread('06-755-006-Ch3-16bit-Reference.tif');

Published with MATLAB® R2023b

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