Any suggestions to calculate the threshold of pixel intensity (the dip represents low intensity)

imshow(matrix(:,:,1))

[x ,y]= ginput(2);

I = matrix(:,:,1);
for i=1:size(matrix,3)
    I=matrix(:,:,i);
    test = improfile(I(:,:,1), [x(1) x(2)] , [y(1)  y(2)]);
end


plot(test);
x1= xline(20, 'color', 'r');
x2=xline(29, 'color', 'b');

[Image Analyst]

What exactly are you looking for? The index where the intensity profile crosses 40? The halfway point from the max intensity to the min intensity?

[BA]

yes, exactly.

Answer 1

[Image Analyst]

Try this:

[cx, xy, profile] = improfile(matrix(:,:,1), [x(1), x(2)] , [y(1), y(2)]);
threshold = (max(profile) + min(profile)) / 2; % Half way point in intensity.
indexLeft = find(profile >= threshold, 1, 'first')
xLeft = cx(indexLeft);
yLeft = cy(indexLeft);
indexRight = find(profile >= threshold, 1, 'last')
xRight = cx(indexRight);
yRight = cy(indexRight);

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[BA]

I tried this, but 'profile' returns the same value of 'test'. Let me explain this: the dip represents 'aperture', so I need to calculate the 'aperture' which varies from context to context.

[Image Analyst]

Give the complete code, not a snippet. And tell me where you clicked on the image.

Yes, I renamed your badly-named "test" variable to a more descriptively -named "profile". But that is not a problem. It will still work.

I don't know what "calculate the 'aperture'" means. I took the profile and found both the x and y location for the threshold at both the left side of the dip and the right side of the dip. What else do you want?

[BA]

Aperture that I need to calculate represents the distance between the tongue and the pharyngeal wall as attached in the image