Apparatus and methods for inspecting a specimen are disclosed. An inspection tool is used at one or more operating modes to obtain images of a plurality of training regions of a specimen, and the training regions are identified as defect-free. Three or more basis training images are derived from the images of the training regions. A classifier is formed based on the three or more basis training images. The inspection system is used at the one or more operating modes to obtain images of a plurality of test regions of a specimen. Three or more basis test images are derived from to the test regions. The classifier is applied to the three or more basis test images to find defects in the test regions.