MATLAB: Counting holes in an image

Question

writing an algorithm that will count the number of holes in the image that do not touch the border

Answer 1

Threshold then call imclearborder() and bwlabel(). Assuming you have dark holes on a bright background:

% Binarize:
binaryImage = grayImage < someValue;
% Remove those touching border
binaryImage = imclearborder(binaryImage);
% Count holes:
[~, numHoles] = bwlabel(binaryImage);