Morphomics via next-generation electron microscopy

Abstract

The living body is composed of innumerable fine and complex structures. 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, which can bias observations. Recently, new trends in EM research have emerged, enabling coverage of far broader, nano-scale fields of view for two-dimensional wide areas and three-dimensional large volumes. Moreover, cutting-edge bioimage informatics conducted via deep learning has accelerated the quantification of complex morphological bioimages. Taken together, these technological and analytical advances have led to the comprehensive acquisition and quantification of cellular morphology, which now arises as a new omics science termed 'morphomics'.

Keywords: 3D bioimaging; comprehensive morphological analysis; deep learning; imaging database; next-generation electron microscopy.

Figure 1

The historical timeline of the EM. Representative milestones in the development of EM are shown.

Figure 2

2D wide-area EM imaging. (A) Wide-area TEM imaging of a mouse kidney sample. Weakly enlarged images (i and ii) show the simultaneous imaging of multiple glomeruli and renal tubules; strongly magnified images (iii and iv) are conventional EM views containing endothelial basement membranes, podocytes, mesangial cells, and epithelial cells. (B) Wide-area SEM imaging of a rat liver section via the backscattered electron detection method. The tiled images provide a view of Kupffer cells, hepatocytes, and endothelial cells in addition to the hepatic lobule with different magnifications.

Figure 3

3D volume EM imaging using AT and SEM. (A) Serial sections of an NB4 cell (an M3 acute myeloid leukaemia cell). The shape of the nucleus is highly variable even within a single cell. (B) 3D reconstruction of the NB4 cell using about 130 serial sections shown in A. The nuclei, cell body, and mitochondria (high electron density organelles) of the cell were segmented. (C) 3D reconstruction of the macula densa in the distal tubules of a mouse kidney glomerulus. The nuclei of the macula densa were segmented.

Figure 4

Overview of morphomics analysis of biological tissue using various imaging approaches. (A) The morphome refers to the totality of the morphological features of cells or tissues in an organism. It is the result of molecular dynamics, including its DNA (genome), RNA (transcriptome), protein (proteome), and metabolic (metabolome) information. (B) Morphologically, various types of tissues, cellular structures, and organelles in the living body range from centimetre to nanometre scales, which can be observed via different imaging techniques. In certain cases, the continuous nature of the morphome cannot be quantified by one microscopy technique alone. To compensate for the weakness of each microscope, a combination of imaging-based methods, known as correlative microscopy mentioned previously, is required to observe the biological nature and process massive amounts of multi-layered morphome data. LM, light microscopy.