bwskel() will almost always leave branches on the skeleton. You have to get rid of them. While you can use the minbranchlength option in the call to bwskel(), the result will usually still have small unpruned branches and spurs, depending on the shape of the skeleton near the corresponding branchpoint. There are other ways to get rid of them, but this is one. It's probably not the most efficient, but it's an example.
load BW_2.mat
BW2 = bwpropfilt(BW, 'perimeter', 1);
BW2 = imfill(BW2,'holes');
skel = bwskel(BW2,'minbranchlength',100); % get rid of most small branches
% remove remaining branches and spurs by pruning only the endpoints close to a branchpoint
skel2 = skel;
ep = bwmorph(skel2,'endpoints');
nendpoints = nnz(ep);
while nendpoints > 2
bp = bwmorph(skel2,'branchpoints');
Db = bwdist(bp); % distance from branchpoints
Deb = Db.*ep; % endpoint distances from closest branchpoint
skel2(Deb == min(nonzeros(Deb))) = false; % remove endpoint that's closest to a branchpoint
ep = bwmorph(skel2,'endpoints');
nendpoints = nnz(ep);
end
% now the skeleton only has two endpoints
[I,J]=find(ep);
imshow(BW,'border','tight')
hold on
scatter(J,I,50,'filled')
There's no guarantee that the pruned skeleton reaches the apparent end of the blob. That statement applies both to the skeleton returned directly from bwskel() and to the skeleton after post-processing.
