How can I extract 3D features form a stack of 2D images?

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May 2017-2-24

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此问题的直接链接

https://ww2.mathworks.cn/matlabcentral/answers/326681-how-can-i-extract-3d-features-form-a-stack-of-2d-images

评论： Image Analyst 2017-3-21

R_006S.zip

I am conducting a lung nodule detection form CT scan images. I extract the nodule candidates form series of 2D CT images. Then I stack the extracted ROIs to get a 3D image. After that I want to extract 3D features, but I don't know how can I extract the features from 3D directly or from each layers of 2D images. Please kindly suggest me how can I extract 3D features form a stack of 2D images.

srcFiles = dir('R_006S\*.jpg');  % the folder in which images exists
n = length(srcFiles);
a={}; slices={};
for i = 1:n
    fileName = strcat('R_006S\',srcFiles(i).name);
    a{i} = imread(fileName);   
    slices{i} = (a{i});
end
X = cat(3,slices{1:end});
map = hsv(90);
XR = X;
Ds = smooth3(XR);
hiso = patch(isosurface(Ds,5),'FaceColor','green','EdgeColor','none');
hcap = patch(isocaps(XR,5),'FaceColor','interp','EdgeColor','none');
colormap(map)
daspect(gca,[1,1,.4])
lightangle(305,30);
fig = gcf;
fig.Renderer = 'zbuffer';
lighting phong
isonormals(Ds,hiso)
hcap.AmbientStrength = .6;
hiso.SpecularColorReflectance = 0;
hiso.SpecularExponent = 50;
ax = gca;
ax.View = [215,30];
ax.Box = 'On';
axis tight
title('Original Data');

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Massimo Zanetti 2017-2-24

编辑：Massimo Zanetti 2017-2-24

在 MATLAB Online 中打开

What do you mean by "exctracting features"? What features are you referrfing to?

PS. In your code there is some redundancy in loading images and making X, consider this to simplify it:

srcFiles = dir('R_006S\*.jpg');  % the folder in which images exists
n = length(srcFiles);
X = zeros(512,512,n);
for i = 1:n
    fileName = ['R_006S\',srcFiles(i).name];
    X(:,:,i) = imread(fileName);
end

Now X is your 3D image.

May 2017-3-4

Thank you for your suggest. I want to extract the shape (round or not), volume, diameter, contrast and stolidity of VOI.

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Answer 1

Image Analyst 2017-3-4

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Do something (filtering or whatever is needed) to get to a point where you can threshold. Then threshold, label, and call regionprops().

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May 2017-3-5

Thank you so much, Image Analyst.

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Answer 2

MDanit 2017-3-15

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Could you please provide your full answer here? As I have the same problem.

Thanks,

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MDanit 2017-3-21

编辑：MDanit 2017-3-21

Thanks for your comments! Image Analyst, I have different stacks from a single cell and I want to reconstruct the 3d image of cell using those stacks so that I can extract data from its surface in form of (x, y, z). Do you possibly have any idea? Thanks,