Hi Marijke, thanks for your post!  The best way to estimate amyloid plaque load in brain tissue is to use the Area Fraction Fractionator probe.  The results of this probe will give you the estimate of area and volume of plaques as well as the area and volume of normal tissue for comparison.  In our new Version 9 release, we have a great new feature making the AFF easier to perform by having the middle mouse button place a second marker type allowing you to mark both plaques and normal tissue without having to switch markers while marking.  I hope this helps, let us know if you need any more info.