Bioimaging for quantitative phenotype analysis

•We review major applications of bioimage-based quantitative phenotype analysis.•Phenotypes include cellular, tissue, organismal, behaviorial and facial phenotypes.•We describe biological questions and experimental needs addressed by such analysis.•We review computational techniques and tools that are available in these contexts. With the development of bio-imaging techniques, an increasing number of studies apply these techniques to generate a myriad of image data. Its applications range from quantification of cellular, tissue, organismal and behavioral phenotypes of model organisms, to human facial phenotypes. The bio-imaging approaches to automatically detect, quantify, and profile phenotypic changes related to specific biological questions open new doors to studying phenotype-genotype associations and to precisely evaluating molecular changes associated with quantitative phenotypes. Here, we review major applications of bioimage-based quantitative phenotype analysis. Specifically, we describe the biological questions and experimental needs addressable by these analyses, computational techniques and tools that are available in these contexts, and the new perspectives on phenotype-genotype association uncovered by such analyses.