Abstract: Methods and systems for high dynamic range (HDR) charged particle analysis using clustering processes include accessing a plurality of instances of image data for a region of a sample, where each instance of image data was captured with different parameters by a charged particle microscope. The difference in parameters may include one or more of a difference in contrast, brightness, beam strength, beam type, gamma, and/or a combination thereof. An HDR charged particle microscopy data structure is then generated using the captured image data, and one or more features of the sample are identified based on the HDR charged particle microscopy data structure. In some methods according to the present invention, the methods further include performing EDS analysis on the sample based on the determined one or more identified features.

Abstract: Methods of aligning specimen images of specimen sections situated on a substrate include obtaining an optical or SEM image of the substrate and locating and aligning optical or SEM images of each specimen section. The specimen sections are then imaged with an SEM to obtain preview images, and a region of interest (ROI) in at least one of the preview images is selected. The preview images are processed so that at least portions of the preview images proximate the ROI are aligned. Based on the alignment of the preview images, final SEM image of selected specimen sections are obtained so that a set of images aligned in three dimensions is available. Image alignment can use cross-correlation with a fixed or variable reference that can be updated as specimen section images are processed.