Light microscopy applications in systems biology: opportunities and challenges
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REVIEW
Open Access
Light microscopy applications in systems biology: opportunities and challenges Paul Michel Aloyse Antony1*, Christophe Trefois1, Aleksandar Stojanovic2, Aidos Sagatovich Baumuratov1 and Karol Kozak3,4
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. Keywords: Microscopy, Systems biology, Image analysis, Segmentation, Features, Machine learning
Introduction Humans are essentially a visual species. Most of our sensory neocortex is engaged in the processing of visual inputs that we gather from our surroundings. Not surprisingly, visualization techniques are at the heart of science and engineering [1]. One of the ultimate goals of systems biology is to elucidate relationships between molecular system states and higher order phenotypic traits. However, light scattering and other optical properties of living matter complicate the acquisition of informative images. For many decades, chemical fixation and the slicing of biological matter have been used to improve the stability and optical properties of samples. However, understanding living dynamic biological systems by examining fixed specimens is, at the best, a heuristic process. The main challenge of the post-genomic era is understanding the rules governing dynamic biological systems. Current genomic tools in combination with advances in microscopy and computation facilitate in vivo observations of any genetic entity of interest. Recent progress in * Correspondence: [email protected] 1 Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg Full list of author information is available at the end of the article
biotechnology, technology, and interdisciplinary cooperation provides more realistic insights into biological processes than ever before. With regard to systems biology, microscopy is a tool that connects multiple scales of biological complexity, ranging from molecules to populations. Recent progress in light microscopy allows for unprecedented insights into nanostructures, as well as unprecedented experimental throughput. In addition, high-resolution three-dimensional (3D) imag
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