Yes I have used this software to isolate proteins differentially expressed between treatment groups of 2D gels. Can you please elucidate where you are having problems? I found it best to warp the images by selecting manual anchors before forming the fusion image. The comparison of protein output can then be made between various groups of the gels. How many gels do you have to analyse? Have you got a pooled sample or reference gel of use? It is best to map the gels to a reference with most number of clear spots.