take largest connected components in 2D slices and then reconstruct the 3D by stacking them

Question

banikr 2020-4-23

0
链接

此问题的直接链接

https://ww2.mathworks.cn/matlabcentral/answers/520307-take-largest-connected-components-in-2d-slices-and-then-reconstruct-the-3d-by-stacking-them

评论： banikr 2020-4-26

Hello,

I am doing some morphological image processing. I want to remove the 4 unwanted blobs from the binary object(image below)

If I axially slice the image, I can take the largest connected component and exclude others like the image below:

I have tried the following codes which results binary size mismatch issues.

ind = 1;
sz = size(bi) % bi is the 3D mask with dimension: 170x256x100
final_mask = zeros(sz) 
for i = 1:sz(3) %taking the 2D axial slice iterations->  1:100
    cc = bwconncomp(bi(:,:,i)); 
%     disp(cc)
    S = regionprops(cc, 'Area', 'PixelIdxList');%'Centroid');
    ax_slice = zeros(sz(1), sz(2));
    numPixels = cellfun(@numel, cc.PixelIdxList);
%     disp(numPixels)
    [biggest,idx] = max(numPixels); % taking the largest component number of pixels and their indices
    ax_slice(cc.PixelIdxList{idx})= 1;
    final_mask(:,:,i) = ax_slice;
end

https://drive.matlab.com/sharing/ab1343a8-a5ce-4f10-9f2b-4d518d752716

or

bi_copy.zip

I have shared the bi_copy.mat in the link above.

Please let me know how to deal with it.

Thanks.

0 个评论
显示 -2更早的评论隐藏 -2更早的评论

请先登录，再进行评论。

请先登录，再回答此问题。

Answer 1

darova 2020-4-24

1
链接

此回答的直接链接

https://ww2.mathworks.cn/matlabcentral/answers/520307-take-largest-connected-components-in-2d-slices-and-then-reconstruct-the-3d-by-stacking-them#answer_428190

erode image
dilate image

clc                         % clear command window
cla                         % clear axes
bi11 = bi;                  % create copy of 'bi'
bi1 = bi(:,:,170:end);      % get top part
R = 2;                      % radius of structuring element
[x,y,z] = meshgrid(-R:R);   % X Y Z 3d matrices
el = x.^2+y.^2+z.^2 <= R^2; % sphere of radius 'R'
bi2 = imerode(bi1, el);     % erode image
bi3 = imdilate(bi2, el);    % dilate image
bi11(:,:,170:end) = bi3;    % replace original top part
isosurface(bi11,.95)        % display 3d image
axis vis3d
light