Removing background and measuring image functions in MATLAB

Question

I am trying to measure the areas of each particle shown in this image:

I managed to get the general shape of each particle using the MSER shown here:

but I'm having trouble removing the background. I tried using MATLAB imfill, but it does not fill all the particles, because some are cut off at the edges. Any tips on how to get rid of the background or find particle areas in some other way? Greetings.

Edit: this is what imfill looks imfill :

Edit 2: Here is the code used to get the outline. I used this one for MSER.

 %Compute region seeds and elliptial frames. %MinDiversity = how similar to its parent MSER the region is %MaxVariation = stability of the region %BrightOnDark is used as the void is primarily dark. It also prevents dark %patches in the void being detected. [r,f] = vl_mser(I,'MinDiversity',0.7,... 'MaxVariation',0.2,... 'Delta',10,... 'BrightOnDark',1,'DarkOnBright',0) ; %Plot region frames, but not used right now %f = vl_ertr(f) ; %vl_plotframe(f) ; %Plot MSERs M = zeros(size(I)) ; %M = no of overlapping extremal regions for x=r' s = vl_erfill(I,x) ; M(s) = M(s) + 1; end %Display region boundaries figure(1) ; clf ; imagesc(I) ; hold on ; axis equal off; colormap gray ; %Create contour plot using the values %0:max(M(:))+.5 is the no of contour levels. Only level 0 is needed so %[0 0] is used. [c,h]=contour(M,[0 0]) ;; set(h,'color','r','linewidth',1) ; %Retrieve the image data from the contour image f = getframe; I2 = f.cdata; %Convert the image into binary; the red outlines are while while the rest %is black. I2 = all(bsxfun(@eq,I2,reshape([255 0 0],[1 1 3])),3); I2 = imcrop(I2,[20 1 395 343]); imshow(~I2); 

Answer 1

Proposed Solution / Trick and Code

It seems you can work with M here. One trick you can use here is to fill in the zeros along all the borders of the image M , and then fill its holes. This will take care to fill the drops that touched the borders before, since now there will be no blob touching the borders due to filling the zeros.

So, after you have M , you can add this code -

 %// Get a binary version of M M_bw = im2bw(M); %// Pad zeros all across the grayscale image padlen = 2; %// length of zeros padding M_pad = padarray(M_bw,[padlen padlen],0); %// Fill the holes M_pad_filled = imfill(M_pad,'holes'); %// Get the background mask after the holes are gone background_mask = ~M_pad_filled(padlen+1:end-padlen,padlen+1:end-padlen); %// Overlay the background mask on the original image to show that you have %// a working background mask for use I(background_mask) = 0; figure,imshow(I) 

results

Input Image -

Foreground mask (this will be ~background_mask ) -

Output Image -