1. A wafer inspection system, comprising: an optical subsystem configured to scan a wafer thereby generating image patches in inspection image frames for the wafer; and one or more computer subsystems coupled to the optical subsystem, wherein the one or more computer subsystems are configured for: aligning each of the image patches in each of the inspection image frames to design information for the wafer; detecting defects in the image patches; deriving multiple layer design attributes at locations of the defects from the image patches corresponding to the locations of the defects; building a binning method with the multiple layer design attributes, wherein the binning method separates the defects into bins with different yield impacts on a device being formed on the wafer, and wherein the binning method is built such that the defects that are one type of defects of interest and have a first of the different yield impacts are separated into a first of the bins and the defects that are the one type of the defects of interest and have a second of the different yield impacts are separated into a second of the bins; and binning the defects with the binning method to thereby separate the defects into the bins with the different yield impacts on the device being formed on the wafer and to separate the one type of the detects of interest having the first of the different yield impacts into the first of the bins and the one type of the defects of interest having the second of the different yield impacts into the second of the bins.