Create an image stack (3-D matrix)

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Jack
Jack 2013-6-4
编辑： DGM 2023-2-13
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 个评论
joseph robinson
joseph robinson 2017-4-19
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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采纳的回答

Kye Taylor
Kye Taylor 2013-6-4
编辑：Kye Taylor 2013-6-4
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});

更多回答（2 个）

hf fh
hf fh 2018-5-21
编辑：DGM 2023-2-12
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 ...
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Walter Roberson
Walter Roberson 2021-8-16
编辑：Walter Roberson 2021-8-16
@jaydip sawant
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 2022-2-18
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 2013-6-4
编辑：Image Analyst 2013-6-4
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 个评论
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Jay Kandukuri
Jay Kandukuri 2021-7-30
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 2021-7-31
@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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