The simplest implementation of MSER happens to be this one using the C API. There's another listing from the Google SoC here using the C++ API.
I guess your best way to compare results would be to implement the code in any of the above links. Comparing the results with Matlab is generally a good thing, as we can expect that to be a standard (more or less). VlFeat has a library with both C and Matlab interfaces that has MSER functions. The last link also has a brief explanation from where you might be able to understand which "data" to compare. What sort of comparison do you have in mind - if it's similarity between regions in two different images, then using a Gray level Co-occurrence Matrix (GLCM) of the regions should work. The MSER will give you the regions, but comparison may not require further data of MSER.
Did you use the OpenCV cvMSER()
function btw, or code the entire thing?