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

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');

[Massimo Zanetti]

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]

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

Answer 1

[Image Analyst]

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

[May]

Thank you so much, Image Analyst.

Answer 2

[MDanit]

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

Thanks,

[May]

I extracted geometric measures using the code from the link below and some 3D features from regionprops(). https://www.mathworks.com/matlabcentral/fileexchange/33690-geometric-measures-in-2d-3d-images

Good Luck!

[Image Analyst]

Mina, see my Image Segmentation Tutorial : http://www.mathworks.com/matlabcentral/fileexchange/?term=authorid%3A31862

[MDanit]

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,

[Image Analyst]

You can bring it into Avizo: https://www.fei.com/software/avizo-3d/