Automated morphological phenotyping using learned shape descriptors and functional maps: A novel approach to geometric morphometrics

The methods of geometric morphometrics are commonly used to quantify morphology in a broad range of biological sciences. The application of these methods to large datasets is constrained by manual landmark placement limiting the number of landmarks and introducing observer bias. To move the field forward, we need to automate morphological phenotyping in ways that capture comprehensive representations of morphological variation with minimal observer bias. Here, we present Morphological Variation Quantifier (morphVQ), a shape analysis pipeline for quantifying, analyzing, and exploring shape variation in the functional domain. morphVQ uses descriptor learning to estimate the functional correspondence between whole triangular meshes in lieu of landmark configurations. With functional maps between pairs of specimens in a dataset we can analyze and explore shape variation. morphVQ uses Consistent ZoomOut refinement to improve these functional maps and produce a new representation of shape variation, area-based and conformal (angular) latent shape space differences (LSSDs). We compare this new representation of shape variation to shape variables obtained via manual digitization and auto3DGM, an existing approach to automated morphological phenotyping. We find that LSSDs compare favorably to modern 3DGM and auto3DGM while being more computationally efficient. By characterizing whole surfaces, our method incorporates more morphological detail in shape analysis. We can classify known biological groupings, such as Genus affiliation with comparable accuracy. The shape spaces produced by our method are similar to those produced by modern 3DGM and to auto3DGM, and distinctiveness functions derived from LSSDs show us how shape variation differs between groups. morphVQ can capture shape in an automated fashion while avoiding the limitations of manually digitized landmarks, and thus represents a novel and computationally efficient addition to the geometric morphometrics toolkit. Author summaryThe quantification of biological shape variation has relied on expert placement of relatively small subsets of landmarks and their analysis using tools of geometric morphometrics (GM). This paper introduces morphVQ, a novel, automated, learning-based approach to shape analysis that approximates the non-rigid correspondence between surface models of bone. With accurate functional correspondence between bones, we can characterize the shape variation within a dataset. Our results demonstrate that morphVQ performs similarly to manual digitization and to an existing automated phenotyping approach, auto3DGM. morphVQ has the advantages of greater computational efficiency and while capturing shape variation directly from surface model representations of bone. We can classify biological shapes to the Genus level with comparable accuracy to previous approaches, and we can demonstrate which aspects of bone shape differ most between groups. The ability to provide comparable accuracy in a Genus level classification with features extracted from morphVQ further guarantees the validity of this approach.