I am not familiar with Sigmascan pro software which I guess can do many image processing and analysis tasks other than disease symptoms on leaves. In my opinion it is easier if you try to use free image processing and analysis packages such as Orfeo, Monteverdi and you can find the image processing tool in MATLAB very useful. I refer you to the following paper which deals with the same problem and uses MATLAB.
Jayme Garcia Arnal Barbedo,Digital image processing techniques for detecting, quantifying and classifying plant diseases, Springerplus. 2013; 2: 660.
ImageJ is a powerful and versatile but complex software for this. There are lots of plugins so that it's really a multi-purpose software with a vivid community which can help.
I would echo Peter's thoughts on ImageJ. My colleagues here at the University have had good success using this for different needs related to processing images with different severities, and they linked it with R to be able to process the results in real-time. We are currently working to build directly into this system other calculations and analyses. Complex, yes, but very useful.