Automated analysis of High‐content Microscopy data with Deep Learning

Advances in automated image acquisition and analysis, coupled with the availability of reagents for genome‐scale perturbation, have enabled systematic analyses of cellular and subcellular phenotypes (Mattiazzi Usaj et al, 2016). One powerful application of microscopy‐based assays involves assessment of changes in the subcellular localization or abundance of fluorescently labeled proteins in response to various genetic lesions or environmental insults (Laufer et al, 2013; Ljosa et al, 2013; Chong et al, 2015). Proteins localize to regions of the cell where they are required to carry out specific functions, and a change in protein localization following a genetic or environmental perturbation often reflects a critical role of the protein in a biological response of interest. High‐throughput (HTP) microscopy enables analysis of proteome‐wide changes in protein localization in different conditions, providing data with the spatiotemporal resolution that is needed to understand the dynamics of biological systems. The budding yeast, Saccharomyces cerevisiae, remains a premiere model system for the development of experimental and computational pipelines for HTP phenotypic analysis.