Light microscopy applications in systems biology: opportunities and challenges

Abstract

Biological systems present multiple scales of complexity, ranging from molecules to entire populations. Light microscopy is one of the least invasive techniques used to access information from various biological scales in living cells. The combination of molecular biology and imaging provides a bottom-up tool for direct insight into how molecular processes work on a cellular scale. However, imaging can also be used as a top-down approach to study the behavior of a system without detailed prior knowledge about its underlying molecular mechanisms. In this review, we highlight the recent developments on microscopy-based systems analyses and discuss the complementary opportunities and different challenges with high-content screening and high-throughput imaging. Furthermore, we provide a comprehensive overview of the available platforms that can be used for image analysis, which enable community-driven efforts in the development of image-based systems biology.

Figure 1

Factors to be considered for the success of microscopy-based projects: The development of highly specialized microscopes has improved the quality of raw data in image-based projects. However, optimal results are based on the choice of adequate imaging systems. A complete overview of available imaging technologies is beyond the scope of this review. However, as a guideline, the choice of an adequate microscope is based on sample- and project-specific factors. The optics of the microscope need to acquire images with adequate resolution and penetration depth, and a level of acceptable phototoxic stress needs to be considered for the illumination of the sample. At the level of project management, the needed throughput, which tends to be high in systems biology, needs to be considered, and an adequate image analysis infrastructure needs to be in place to avoid bottlenecks in image analysis and the interpretation of data.

Figure 2

Selected microscopy applications in systems biomedicine: (A), (B), and (C) Analysis of mitotic events by hidden Markov modeling to evaluate mitotic phase transitions [33]. (A) Trellis diagram showing class prediction estimates for a given cell. (B) Event order map and example of time-series images. (C) Double-stained HeLa cells in different cell division states. (D) and (E) Nematode morphology analysis. (D) Automated segmentation of single worms [34]. (E) Straightening of single nematode datasets [35]. (I) and (J) Body atlas for zebrafish [36]. (I) TH-expressing zones are highlighted in green. (J) Registration of single image information into a zebrafish body-atlas database. (F), (G), and (H) In vivo imaging of mice. (F) Miniaturized microscope weighing 1.9 g [37]. (G) Dynamic analysis of the intestinal mucosal barrier function [38]. (H) Nanoscopy of dendritic spine dynamics in the brain of a living mouse [25]. All images were used with permission of the publishers.