problem with watershed 3D segmentation

Question

MARIA RODRIGUEZ SANZ 2018-7-11

0
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此问题的直接链接

https://ww2.mathworks.cn/matlabcentral/answers/409807-problem-with-watershed-3d-segmentation

编辑： raym 2022-1-6

I_mod.mat

Hello!

I have a question related to 3D image segmentation (in order to obtain volume properties). I would like to segment a 3d grayscale image (of some structures in the nuclei of a cell). Watershed segmentation combined with imextended max (as shown in this example: https://blogs.mathworks.com/steve/2006/06/02/cell-segmentation/) yielded excellent results in each 2d "stack" of this 3d construction. Now, I want to implement the same procedure in order to analyse the 3D image (working with volume instead of surfaces). After several tests I have been able to create a nice object (I_mod) to undergo watershed segmentation (the equivalent 3D object that I use in 2D analyses). Unfortunately, to my despair, applying watershed to my object results in a completely black 3d Image. Does anybody have an idea of what's happening?? :(. Wy is this not working with 3D? I have also attached the I_mod object, wich can be visualized by: implay(I_mod,2);

Here is my syntax:

 ---------------------------------------------------------------------------------
if true
  % code
      %CREATE A 3D OBJECT FROM 2D IMAGES:
      image3d= data{1,4}{2,1}{1,1};
      for i=3:2:length(data{1,4}{2,1})
      image3d=cat(3,image3d,data{1,4}{2,1}{i});
      end
      %FILTER AND BINARIZE 3D IMAGE
      filt=medfilt3(image3d);
      filt=imclose(filt, ones(5,5));
      T = graythresh(filt);
      bw_3d = imbinarize(filt,T);
      %OBTAIN PERIMETER OF THE BINARIZED 3D IMAGE
      bw_perim = bwperim(bw_3d);
      %FIND IMEXTENDED OF EACH ORIGINAL 2D IMAGES:
      peaks={}
      for i=1:2:length(data{1,4}{2,1})
          aj=imadjust(data{1,4}{2,1}{i},[0.3  1],[0  1]);
          mask_em = imextendedmax(aj,9000);
          SE = strel('disk', 3)
          mask_em_dil=imdilate(mask_em,SE);
          peaks=[peaks,mask_em_dil];
      end
      %3D RECONSTRUCTION OF PEAKS
      peaks3d= peaks{1};
      for i=2:length(peaks)
      peaks3d=cat(3,peaks3d,peaks{i});
      end
      %OBTAIN COMPLEMENT IMAGE IN 3D
      I_eq_c = imcomplement(image3d);
      %Modify the image so that the background pixels and the extended maxima pixels are forced to be the only local minima in the image.
      I_mod = imimposemin(I_eq_c, ~bw_3d | picos3d);
      implay(I_mod,2);  %The object here is really nice to undergo watershed transformation (as far as I know).
      %APPLY WATERSHED TRANSFORMATION
      L = watershed(I_mod);
      implay(L,2);    %the video shows a completely black 3d resut. (no segments)

Thank you vety much in advance!

Maria

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XF 2019-4-17

Hi, have you solved thie problem? I have the same problem with you now, after (3d)watershed, when I impaly it , it is all black too. Could you please tell me how to solve this? Thank you !

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