I tried OMeR yesterday, it works great, but one thing...
My scanner scans in greyscale. If you let OMeR do the conversion from grey to black and white, it does a real bad job.
If first you load the grey scan into a photo editor such as GIMP and increase the contrast to the point that the paper looks pure white, that is, all the way up if you have to... Then give that to OMeR to convert to B&W, it then does a great job.