Skeletonize 3d cylinders

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Carson Purnell
Carson Purnell 2022-10-28
评论： Matt J 2022-11-4
I'm having trouble figuring out a reliable way to draw lines marking the midpoints of mostly hollow cylinders in a 3d volume. Demo volume attached. I've been trying mostly morpholigical operations (dilate/erode/close/open) to try to finagle out a 'rod' from the cylinder's extent. It's not terrible, but a few get lost and a few get smushed together into a bit of nonsense every time. It's also inflexible and needs handholding with different sizes. Is there a clever way of doing this, hopefully that also avoids spending 95% of the time on super slow dilate operations?
The cylinders are open-ended tubes, so I can't just fill them then erode. I would love to be able to fill them, though. The cylinders also sometimes have junk in them. This makes it nonviable to try to subtract an expanded cylinder from a filled one to generate the rod. I've also tried 3d convolution/template matching and various clustering/watershed methods of breaking smushed regions apart, but it didn't get me any further.
Is there some neat trick that can fill the cylinders, or otherwise identify them with very high accuracy and specificity?
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DGM
DGM 2022-11-4
编辑：DGM 2022-11-4
raw appears to be a volumetric image, but it's 'double', scaled [0 1725], so I don't know how volume viewer would treat it. I'm not used to doing anything technical with volumetric images, but it looks like this:
... which would have the following mean projections:
Matt J
Matt J 2022-11-4
With volshow(raw>0),

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Matt J
Matt J 2022-11-4
编辑：Matt J 2022-11-4
The key problem is that some of the cylinders are touching other cylinders. For those that don't, we can easily separate them with regionprops3 and fit cylinders to them using this FEX download:
https://www.mathworks.com/matlabcentral/fileexchange/87584-object-oriented-tools-for-fitting-conics-and-quadrics
Once you have a cylinder fit, it is easy to derive the medial line. Maybe you can refine the code below with your watershed code to get a better separation of the cylinders
load('democylinders.mat');
BW=imopen(raw>0,strel('sphere',3));
cv=regionprops3(BW,'VoxelList');
cv=cellfun(@transpose, cv{:,1}','un',0);
fobj=cellfun(@cylindricalFit,cv);
fobj=fobj(abs([fobj.radius]-9)<2); %discard cylinder fits giving outlier radii
for i=1:N
surf(fobj(i)); hold on
medialLine(fobj(i));
end; hold off; grid on
axis equal
function medialLine(cyl)
%Plot medial line of a cylinder fit
d=cyl.R(:,1)'*cyl.height/2;
p1=cyl.center+d;
p2=cyl.center-d;
XYZ=num2cell([p1;p2],1);
plot3(XYZ{:},':b','LineWidth',3);
end

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