Wafer images and related alignment methods for crystalline wafers are disclosed. Certain aspects relate to accessing and aligning images of a same or similar crystalline wafer captured from different imaging sources. Alignment may include determining spatial differences between shared crystalline features in various wafer images of the same or similar crystalline wafer and transforming at least one of the images according to the determined spatial differences. With sufficient alignment, information may be associated and/or transferred between the various images, thereby providing the capability of forming a combined wafer image and sub-images thereof with high resolution and spatial coordination between different image sources. Certain aspects relate to development of nondestructive, high fidelity defect characterization and/or dislocation counting methods in crystalline materials based on modern deep convolutional neural networks (DCNN).