MATLAB: How to stack several .tiff files into a 3D stack in .mat format

3d stacktiff

I have attained several tiff images from a microCT scanner and want to be able to stack them in a 3D matrix as a .mat format enable me to analysis them in a DVC simulator. How do I do this?

Best Answer

dinfo = dir('*.tiff');
num_files = length(dinfo);
for K = num_files : -1 : 1     %backwards is more efficient
  thisname = dinfo(K).name;
  thisimage = imread(thisname);
  all_images(:,:,K) = thisimage;
end
save('AllImages.mat', 'all_images');

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MATLAB: How to save image stacks to a .mat file that is readable

Get rid of the fopen() and fwrite(). Just use save():

After your for loop (where you create ImageStack), just write ImageStack out all in one line:

fullFileName = fullfile(folder, 'ImageStack.mat');
save(fullFileName, 'ImageStack'); 
% Note: save() overwrites/destroys any existing file (does not "add/append").

MATLAB: Overlapping .tiff images

Kind of hard to guess since you didn't attach any of the images. But I'd try to add them all up and then use rgb2ind(). If they are uint8 you'll have to cast to uint16 first. Or you mgiht try binarizing them first. Or cast them to double and add them up and divide by the number of images and then cast back to uint8, and then use rgb2ind. Like I said, hard to say until I see your images and you/I try some things.

Best Answer

Related Solutions

MATLAB: How to save image stacks to a .mat file that is readable

MATLAB: Overlapping .tiff images

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