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    <p>The initial image seems to be well contrasted and I guess we can simply threshold to obtain a good estimate of the cells. Here is a morphological area based filtering of the thresholded image:</p> <p>Threshold: <img src="https://i.stack.imgur.com/Z91Js.png" alt="Threshold at 10"> </p> <p>Area based opening filter(this needs to be set based on your dataset of cells under study): <img src="https://i.stack.imgur.com/y4BCR.png" alt="Size smaller than 2500 pixels removed"></p> <p>Area based closing filter(this needs to be set based on your dataset of cells under study): <img src="https://i.stack.imgur.com/RGSgi.png" alt="enter image description here"></p> <p>Contours using I-Erosion(I): <img src="https://i.stack.imgur.com/Jcony.png" alt="enter image description here"></p> <p>Code snippet: </p> <pre><code>C is input image C10 = C&gt;10; %threshold depends on the average contrast in your dataset C10_areaopen = bwareaopen(C10,2500); %area filters average remove small components that are not cells C10_areaopenclose = ~bwareaopen(~C10_areaopen,100); %area filter fills holes se = strel('disk',1); figure, imshow(C10_areaopenclose-imerode(C10_areaopenclose,se)) %inner contour </code></pre> <p>To get smoother shapes I guess fine opening operations can be performed on the filtered images, thus removing any concave parts of the cells. Also for cells that are attached one could use the distance function and the watershed over the distance function to obtain segmentations of the cells: <a href="http://www.ias-iss.org/ojs/IAS/article/viewFile/862/765" rel="nofollow noreferrer">http://www.ias-iss.org/ojs/IAS/article/viewFile/862/765</a></p> <p>I guess this can be also used on your probability/confidence maps to perform nonlinear area based filtering.</p>
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    1. POContour completion in image segmentation
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    1. COThanks! Could you explain in more detail how I might use this approach on the probability maps?
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    2. COYou could try filling in contours of your probability map using _holefilling_: [imfill](http://www.mathworks.fr/fr/help/images/ref/imfill.html) with the area based filtering as seen in the original solution!
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