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

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.

[Mia Grahn]

Were you able to find a method?

Answer 1

[Chunru]

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
slice(X,Y,Z,V,xslice,yslice,zslice)

% if you don't hnow X, Y, you can use index value along x and y axes.

Answer 2

[r r]

%https://www.mathworks.com/matlabcentral/answers/403570-how-to-make-a-3d-volume-out-of-a-2d-tiff-stack
%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) + "%");
end
% The app volumeViewer will handle the visualization
volumeViewer(stack);

[Walter Roberson]

I would suggest the for loop should be 2:D to avoid re-reading the first image.

Answer 3

[r r]

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

https://www.mathworks.com/matlabcentral/answers/403570-how-to-make-a-3d-volume-out-of-a-2d-tiff-stack

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);
    else
        imwrite(indI,cm,filename,'gif','WriteMode','append','DelayTime', 0.05);
    end
end

Now I want to insert it in 3D to compare it with another 3D model in Matlab? I find it difficult

[Walter Roberson]

%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);
end

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.