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In my understanding MSER.cpp detects both 'black on white' and 'white on black' MSERs. See routine extractMSER_8UC1() which calls both versions and can be modified with a bespoke compilation to detect only one type of MSER.

In my opinion, the main calling MSER procedure should be controlled by a flag to detect 'black on white', 'white on black' OR both types of MSERs.

Either way the documentation should be updated to make clear the performance and how it can be altered if a user requires it.