Does anyone know how to calculate MIP of a 3D image????
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This may sound obvious, but did you look at the max() function? It can take a 3D array and give you the max along any dimension you specify.
% Generate sample 3D array A = rand(2,2,2) % Get maximum intensity projection. mip = max(A, , 3)
In the command window:
A(:,:,1) = 0.6352 0.9889 0.4384 0.9632 A(:,:,2) = 0.2460 0.6582 0.4045 0.9417 mip = 0.6352 0.9889 0.4384 0.9632
I will assume for this discussion that your RGB image stack is arranged as (X, Y, RGB, Z) and that it is named Stack
grayStack = squeeze( 0.2989 * Stack(:,:,1,:) + 0.5870 * Stack(:,:,2,:) + 0.1140 * Stack(:,:,3,:) ); %X, Y, Z after squeeze
[maxgray, maxidx] = max(grayStack, , 3); %along the 3rd axis (Z)
nX = size(Stack,1); nY = size(Stack,2); [X, Y] = ndgrid( 1 : nX, 1 : nY );
MIP_R = Stack( sub2idx( size(Stack), X(:), Y(:), 1, maxidx(:) ) ); MIP_G = Stack( sub2idx( size(Stack), X(:), Y(:), 2, maxidx(:) ) ); MIP_B = Stack( sub2idx( size(Stack), X(:), Y(:), 3, maxidx(:) ) );
MIP = cat(3, reshape(MIP_R, nX, nY), reshape(MIP_G, nX, nY), reshape(MIP_B, nX, nY) );
There are performance tweaks that can be done.
The code would be slightly different if the RGB is the 4th dimension instead of the third.
The first line of the code is effectively doing an rgb2gray() but for all of the image layer simultaneously. This conversion calculates the intensity (brightness) of each pixel in each slice. In the discussion with IA, the conversion from RGB to brightness (intensity) is not done, so the code there is not doing a Maximum Intensity Mapping. You should not be calculating the maximum R along the stack and the maximum G along the stack independently: you need the R, G, and B information combined at each pixel in order to calculate intensity there.
With intensity in hand, the code finds the maximum intensity along the Z, and the Z slice number that corresponds to the brightest point.
Once the slice number is done, there is some code that, in a vectorized way, pulls out the R, G, and B pixel values of the appropriate Z layer. And once it has those, it combines the three channels into a single RGB image.