Create an image stack (3-D matrix)

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!

[joseph robinson]

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!

Answer 1

[Kye Taylor]

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});

Answer 2

[hf fh]

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 ...

[hf fh]

Hi

I have a question

I used the same method but I want to extract it in size format volume like figure 3D

how it would be???

folder = '/Users/mac/Desktop/fiel2/data';
D = '/Users/mac/Desktop/fiel2/data';

for i=1:8
    % {} = cell array
    images{i} = imread(sprintf('%d.tif',i));
    
    I{i} = rgb2gray(images{i});
    I = cat(3, I, images{i});  % Tack on slice i into a new cell.
end

[Walter Roberson]

Sigh, we wish you would have taken the time to read about formatting code while you were posting in the tutorial about formatting code...

[Walter Roberson]

folder = '/Users/mac/Desktop/fiel2/data';

for i=1:8
   images{i} = imread( fullfile(folder, sprintf('%d.tif',i) ));
   I{i} = rgb2gray(images{i});
end
I = cat(3, I{:});

[Image Analyst]

Why do you want the images or Q cell arrays anyway? Chances are you don't. I never do that. I never create a cell array of a bunch of images and I think you most likely don't need to either. Why do you think you need to???

[hf fh]

Thank you for answering me... I'm a beginner in using MATLAB and I just want to convert 20 images from 2D-two to 3D-three dimensions only. The aim is to convert from 20 images to an only volume 3D Look for of a method to apply the images.

I following steps like this:

First: Must be converted to a size of [300 * 300] pixels

Second: Converted to stack==>2D[300*300*20]

Third: Converted to format==> 3D volume

please help me What do I think about is true ??? and if you have a proposal please help me ..

[PRAKASH JOSHI]

Error using rgb2gray>parse_inputs (line 80)

MAP must be a m x 3 array.

Error in rgb2gray (line 52)

isRGB = parse_inputs(X);

it is showing this error

Please help me out

[Walter Roberson]

for i = 1 : 8
    images{i} = imread( fullfile(folder, sprintf('%d.tif', i) ) );
    if ndims(images{i}) > 2
        I{i} = rgb2gray(images{i});
    else
        I{i} = images{i};
    end
end

[Adithya Vasudevan]

folder = 'C:\Users\Suraj\Desktop\images\Results';
for i = 109 : 433
    try
        images{i} = imread( fullfile(folder, sprintf('000%d.jpg', i) ) );
    catch
        continue;
    end
    if ndims(images{i}) > 2
        I{i} = rgb2gray(images{i});
    else
        I{i} = images{i};
    end
end
I = cat(3, I{:});
imshow(I{i});
view(3);

Unable to perform assignment because brace indexing is not supported for variables of this type.

Error in test_3D (line 11)

I{i} = images{i};

[Image Analyst]

This works for me:

folder = pwd; % 'C:\Users\Suraj\Desktop\images\Results';
% for k = 109 : 433
% 	fullFileName = fullfile(folder, sprintf('000%d.jpg', k));
for k = 1 : 10
	fullFileName = fullfile(folder, sprintf('%d.jpg', k));
	if ~isfile(fullFileName)
		fprintf('File #%d not found : %s\n', k, fullFileName);
		continue;
	end
	fprintf('Storing image file #%d : %s\n', k, fullFileName);
	% Store the original image, regardless of whether it's RGB or gray scale.
	originalImages{k} = imread(fullFileName);
	% Store the gray scale version of the image.  Convert (if necessary) from RGB to gray scale.
	if ndims(originalImages{k}) > 2
		grayScaleImages{k} = rgb2gray(originalImages{k});
	else
		grayScaleImages{k} = originalImages{k};
	end
end

Change the comments to have it use your images in your folder, and in the range 109 to 433. Better yet, see if you can just use dir() to get a list of only those images that definitely exist.

[jaydip sawant]

hello i have 12 images in 12 direction like 30,60,... 360

i want to make a 3D volume using these images can anyone please help me in this.

[Image Analyst]

@jaydip sawant use cat()

image3d = cat(3, image1, image2, image3, image4, image5, image6, image7, image8, image9, image10, image11, image12);

[jaydip sawant]

@Image Analyst hello thank you for help, when i tried cat function then this error is showing: -

"Error using images.internal.imageDisplayValidateParams>validateCData (line 118)

Multi-plane image inputs must be RGB images of size MxNx3.

Error in images.internal.imageDisplayValidateParams (line 30)

common_args.CData = validateCData(common_args.CData,image_type);

Error in images.internal.imageDisplayParseInputs (line 79)

common_args = images.internal.imageDisplayValidateParams(common_args);

Error in imshow (line 253)

images.internal.imageDisplayParseInputs({'Parent','Border','Reduce'},preparsed_varargin{:});

Error in Untitle (line 12)"

[Walter Roberson]

It sounds to me as if you have 12 color images. If so then get https://www.mathworks.com/matlabcentral/fileexchange/22940-vol3d-v2 and then

image3d = cat(4, image1, image2, image3, image4, image5, image6, image7, image8, image9, image10, image11, image12);
vol3d('CData', image3d)

[ketan kyung hee university]

I have gray scale 12 images

[jaydip sawant]

@Walter Roberson Thank you for reply , I take X-ray images from diffrent angle like 30,60,....,360. I want place these images in it's angle posission like 30 degree image will place at 30 degree and 60 will place at 60 and so on. Then I can make a 3D volume of these 12 images.

I tried cat function but it does not work well it showing error.

my image pixel is 256 height and 248 width. I want make 256X248X12. last 12 is a number of image.

can you please help me in this problem.

[Walter Roberson]

@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]

Use Fiji or imagej it is free software. After spending many days I could not findout correct stacking solution in matlab.

Answer 3

[Image Analyst]

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

[Image Analyst]

Just do something like

folder = '/Users/mac/Desktop/fiel2/data/';
image3d = zeros(300, 300, 20, 'uint8');
for k = 1 : 20
       % Read one image.
       thisImage = imread( fullfile(folder, sprintf('%d.tif', k) ));
       % Store this image in the k'th slice of the 3-D image array.
       image3d(:, :, k) =imresize(thisImage, [300, 300]);
end

[hf fh]

The same method was used and the result was?

Unable to perform assignment because the size of the left side is 300-by-300 and the size of the right side is 300-by-300-by-3.

Error in d (line 7) image3d(:, :, k) =imresize(thisImage, [300, 300]);

[Walter Roberson]

image4d(:, :, :, k) = imresize(thisImage, [300, 300])

[Image Analyst]

I'd assumed that you had gray scale images. They seem to be color and so creating a 4-D image like Walter showed should work. Or else convert the images to gray scale before using cat()

[Jay Kandukuri]

I am trying to convert 80 dcm images into a 3d stack array can you tell me how i can do that.

[Image Analyst]

@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