function [mask Ccell_cent Carea Car Ccirc Cang coords]=actin_mask(I) sigma=6;hsize=[12,12]; h=fspecial('gaussian',hsize,sigma); I2=imfilter(I,h,'replicate'); %figure(1); imshow(I2) BW=edge(I2,'sobel',0.001); %figure(2);imshow(BW) se=strel('disk',6,0); mask=imdilate(BW,se); mask=imfill(mask,'holes'); mask=imerode(mask,se); %figure(3);imshow(mask) cc=bwconncomp(mask); r=regionprops(cc,'Centroid','Area','Perimeter','MajorAxisLength','MinorAxisLength','PixelList','Orientation'); for i=1:cc.NumObjects area(i)=r(i).Area; end [~,ind]=max(area); for i=1:cc.NumObjects if i~=ind mask(cc.PixelIdxList{i})=0; end end Carea=area(ind); Ccell_cent=r(ind).Centroid; Car=r(ind).MajorAxisLength/r(ind).MinorAxisLength; Ccirc=(r(ind).Area*4*pi)/(r(ind).Perimeter^2); Cang=r(ind).Orientation; x=r(ind).PixelList(1,1); y=r(ind).PixelList(1,2); coords=bwtraceboundary(mask,[y x],'N'); % imshow(image) % hold on % plot(coords(:,2),coords(:,1),'m')