To connect regions, you can use imclose()
mask = imclose(mask, true(9)); % Vary the 9 to connect more or less close regions.
To fill regions, you can use imfill():
mask = imfill(mask, 'holes');
To erase things touching the border, you can use imclearborder:
mask = imclearborder(mask);
To extract a specified number of largest blobs, you can use bwareafilt():
mask = bwareafilt(mask, 3); % Extract 3 largest blobs.
To extract blobs of a specified size or larger you can use either bwareafilt(mask, [smallArea, largeArea]) or bwareaopen():
mask = bwareafilt(mask, [2000, 5000]); % Extract blobs between 2000 and 5000 in pixel area.
mask = bwareaopen(mask, 4000); % Extract blobs only 4000 pixels or larger.
