How to get 2d slices from a 3D image.

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Shweta on 13 Jan 2014
Commented: Walter Roberson on 27 Nov 2021
How to get 2D slices from a 3D image? The image is grayscale, it is a .mhd file and the dimensions of the Image matrix after loading into matlab are 179x200x159 single.
  1 Comment
Mia Grahn
Mia Grahn on 20 Jun 2021
Were you able to find a method?

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Answers (3)

Chunru on 20 Jun 2021
From 'doc slice':
[X,Y,Z] = meshgrid(-2:.2:2);
V = X.*exp(-X.^2-Y.^2-Z.^2); % replace this with your 3D data
xslice = [-1.2,0.8,2]; % slices along x
yslice = [];
zslice = 0; % slices along y
% if you don't hnow X, Y, you can use index value along x and y axes.

r r
r r on 21 Nov 2021
%Rafael S.T. Vieira on 1 Jun 2020::How to make a 3D Volume out of a 2D Tiff stack?
fileFolder = '/Users/Desktop/Slice3D';
filePattern = fullfile(fileFolder, '*.jpg');
all_jpg = dir(filePattern);
first_image = imread(all_jpg(1).name);
[W,H] = size(first_image);
D = numel(all_jpg);
stack = zeros(W,H,D);
stack(:,:,1) = first_image;
for i = 1:D
stack(:,:,i) = imread(all_jpg(i).name);
% uncomment next line for seeing the reading progress
% disp(string(i*100.0/D) + "%");
% The app volumeViewer will handle the visualization
  1 Comment
Walter Roberson
Walter Roberson on 21 Nov 2021
I would suggest the for loop should be 2:D to avoid re-reading the first image.

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r r
r r on 21 Nov 2021
Edited: Walter Roberson on 27 Nov 2021
can you help me
What do you suggest to me , plaeas help me .
I have 30 images converted from 2D to 3D
I used in a methode
and using sliceViewer for convert images to save by *gif
s = sliceViewer(stack); %View the data in the slice viewer.
hAx = getAxesHandle(s); %Get the handle of the axes containing the displayed slice.
filename = 'Slice.gif';%Specify the name of the GIF file you want to create.
sliceNums = 1:24;
for idx = sliceNums
% Update slice number
s.SliceNumber = idx;
% Use getframe to capture image
I = getframe(hAx);
[indI,cm] = rgb2ind(I.cdata,256);
% Write frame to the GIF file
if idx == 1
imwrite(indI,cm,filename,'gif','Loopcount',inf,'DelayTime', 0.05);
imwrite(indI,cm,filename,'gif','WriteMode','append','DelayTime', 0.05);
Now I want to insert it in 3D to compare it with another 3D model in Matlab? I find it difficult
  1 Comment
Walter Roberson
Walter Roberson on 27 Nov 2021
%gif animations are pseudocolored, not RGB.
[slices, cmap] = imread(filename, 'index', 'all');
rgbslices = zeros(size(slices,1), size(slices,2), 3, size(slices,4), 'like', slices);
for K = 1 : size(slices,4)
rgbslices(:,:,:,K) = ind2rgb(slices(:,:,:,K), cmap);
Now rgbslices will be rows x columns x 3 x slices .
I would suggest to you that there are easier ways to do this then to use sliceViewer() and write to a file and read back from the file.

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