Analysis and applications of quantitative representations of cell morphology

Morphology is an important, large-scale manifestation of the global state of cells, and is commonly used as a qualitative or quantitative measure of the outcome of various assays. Herein I describe methods for the numerical representation of cell shape, an analysis of the utility of several different cell-shape representations, statistical methods for comparing cell populations of different shapes, and an approach to using statistical models of shape for finding cells in micrographs. In this work, I have found that principal components analysis of shapes represented as geometric outlines provides measures of morphology which are quantitative, biologically meaningful, human interpretable, and work well across a range of cell types and parameter settings. This representation underlies a suite of software tools that I have developed to facilitate shape representation, comparison, visualization, and analysis.