The living body is composed of innumerable fine and complex structures and although these structures have been studied in the past, a vast amount of information pertaining to them still remains unknown. When attempting to observe these ultra-structures, the use of electron microscopy (EM) has become indispensable. However, conventional EM settings are limited to a narrow tissue area that can bias observations. Recently, new trends in EM research have emerged that provide coverage of far broader, nano-scale fields of view for two-dimensional wide areas and three-dimensional large volumes. Together with cutting-edge bioimage informatics conducted via deep learning, such techniques have accelerated the quantification of complex morphological images. Moreover, these advances have led to the comprehensive acquisition and quantification of cellular morphology, which is now treated as a new omics science termed 'morphomics'. Moreover, by incorporating these new methodologies, the field of traditional pathology is expected to advance, potentially with the identification of previously unknown structures, quantification of rare events, reclassification of diseases and automatic diagnosis of diseases. In this review, we discuss these technological and analytical advances, which have arisen from the need to analyse nano-scale bioimages, in detail, as well as focusing on state-of-art image analysis involving deep learning.