Read out intensites and corresponding X,Y,Z-coordinates from a 3D-image

3 views (last 30 days)
Hello,
this is a common problem. But there were no real answers to this question in this forum.
I have a 3D-image generated from a 3D-array - I want to get the intensity values plus their corresponding position (X,Y,Z) in a normal spreadsheet in MatLab.
Ultimately, I would get something like:
Intensity | X | Y | Z
and this for every point in the image.
Since there are millions of points it might be also a good idea to cut out points with 0 intensity.
Has somebody done something similar?
Best wishes.

Accepted Answer

Image Analyst
Image Analyst on 24 Nov 2014
Edited: Image Analyst on 24 Nov 2014
What is the size of the third dimension? If it's 3 then it can be considered a normal RGB color image and you can use impixelinfo() to see the values. If you still want it in a spreadsheet, then I suggest you extract each plane of your volumetric image in a loop and then send that to Excel. If you really, really need the x,y,z values also then I suggest you create an N by 4 array and then write out
[rows, columns, slices] = size(array3D);
array2D = zeros(numel(array3D), 4);
counter = 1;
for z = 1 : slices
for x = 1 : columns
for y = 1 : rows
array2D(counter, :) = [array3D(y, x, z), x, y, z];
counter = counter + 1;
end
end
end
xlswrite(filename, array2D);
  10 Comments
Walter Roberson
Walter Roberson on 8 May 2016
Hesham Shehata comments,
I tried to use this code with various types of images but i always get zero values only! can you please advise how to define the image with this code? thanks for your cooperation.
Image Analyst
Image Analyst on 8 May 2016
Then your image is all zero. Obviously the x, y, and z cannot be printed as zeros - that's impossible.

Sign in to comment.

More Answers (1)

Sean de Wolski
Sean de Wolski on 26 Nov 2014
load mri
D = squeeze(D);
idx = logical(D); % Where in D is nonzero?
vals = D(idx); % extract values
ind = find(idx); % linear index
[row,col,pag] = ind2sub(size(D),ind); % sub indices
xlswrite('file.xlsx',[row col pag vals])

Categories

Find more on Image Processing Toolbox in Help Center and File Exchange

Community Treasure Hunt

Find the treasures in MATLAB Central and discover how the community can help you!

Start Hunting!