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Create an image stack (3-D matrix)

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Jack
Jack on 4 Jun 2013
Edited: DGM on 13 Feb 2023
Hello. I'm importing a series of images from my working directory using the following code:
for i=139:141
% {} = cell array
images{i} = imread(sprintf('IMG_%04d.JPG',i));
I{i} = rgb2gray(images{i});
end
I have a large number of images, but here I'm importing just a sample. I'm converting each color image to grayscale. I must also create an image stack, a 3D matrix of grayscale images. I've been browsing the web for an answer, but I'm having difficulty understanding the process. size(I) yields '1 141', and I'm wondering how I can create a 3-D matrix from this. Your help would be greatly appreciated. Thank you!
  1 Comment
joseph robinson
joseph robinson on 19 Apr 2017
Adding to the feedback of others, your code would be more efficient without looping, e.g.,
idx = 139:141;
# image file paths
ipaths =cellfun(@(x) sprintf('IMG_%04d.JPG',x),idx,'uni',false);
# read images into cell array
I = cellfun(@imread, ipaths,'uni',false);
# Convert to gray-scale
Igray = cellfun(@rgb2gray,I,'uni',false);
# Concatenate 3 gray-scale images into single 3D matrix
myImage = cat(3,Igray{:});
Hope this helps!

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Accepted Answer

Kye Taylor
Kye Taylor on 4 Jun 2013
Edited: Kye Taylor on 4 Jun 2013
Execute this command after your code above to get the three gray-scale images you create into one 3D matrix of grayscale images;
myImage = cat(3,I{139:141});

More Answers (2)

hf fh
hf fh on 21 May 2018
Edited: DGM on 12 Feb 2023
Please help me .. I searched a lot for convert 2Dimages into 3D but I still have the same problem !!! ''I can not get the images in volume in three dimensions" I have a search in 20 image dimensions [773x896]pixel, I want to convert it to 3D-three dimensions in volume form to study the depth, I following steps this:
  1. Must be converted to a size of [300 * 300] pixels
  2. Converted to stack
  3. Converted to format==> 3D
like :
folder = '/Users/mac/Desktop/fiel2/data/';
for i=1:20
images{i} = imread( fullfile(folder, sprintf('%d.tif',i) ));
Q{i}=imresize(images{i} ,[300 , 300]);
end
I = cat(3, Q{i});
imshow(Q{i});
view(3);
Thank you for help me ...
  17 Comments
Walter Roberson
Walter Roberson on 16 Aug 2021
Edited: Walter Roberson on 16 Aug 2021
For your situation, the cat(3) that Image Analyst showed is correct.
Your difficulty is that you cannot use imshow() to display volumes. To display volumes, you need to use one of the following:
  • montage()
  • implay()
  • volumeViewer()
  • vol3d from the FIle Exchange
  • videofig from the File Exchange
Tilkesh
Tilkesh on 18 Feb 2022
Use Fiji or imagej it is free software. After spending many days I could not findout correct stacking solution in matlab.

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Image Analyst
Image Analyst on 4 Jun 2013
Edited: Image Analyst on 4 Jun 2013
The (badly-named) variable I is a one dimensional array of cells. Inside each cell it a 2D array. So, in effect, this is a 3D array though you can't reference it like I(row, column, slice). If that is what you need to do then you need to do
I = []; % Before the loop
Then in the loop:
I = cat(3, I, images{i}); % Tack on slice i into a new cell.
In the meantime, please read the FAQ on cells to get a better idea of how they work: http://matlab.wikia.com/wiki/FAQ#What_is_a_cell_array.3F
  6 Comments
Jay Kandukuri
Jay Kandukuri on 30 Jul 2021
I am trying to convert 80 dcm images into a 3d stack array can you tell me how i can do that.
Image Analyst
Image Analyst on 31 Jul 2021
@Jay Kandukuri, allocate an array of 80 slices, then loop and read in the files and load them in to the array you just allocated.
dcm3d = zeros(rows, columns, 80, 'uint8');
% Then in a loop, load them in
for slice = 1 : 80
thisImage = dcmread(filename); % filename must change on every iteration obviously.
dcm3d(:, :, slice) = thisImage;
end

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