A Method to the Madness: Using Persistent Homology to Measure Plant Morphology

Extract

As the study of plant variation and characterization moves from measurements of largely organismal-level polymorphisms to those of cellular- and molecular-level traits, the need for morphological measuring tools that incorporate complex trait information is clear. While quantitative methodologies have improved, current methods rely on the researcher evaluating what morphological metrics to measure, and this results in a somewhat biased collection of values for univariate or multivariate analysis (Topp et al., 2013). The models that rely on the compilation of standard univariate measurements are not flexible enough to accommodate a large amount of variation in plant traits, which limits our understanding of genetic and environmental contributions to plant morphology (Chitwood and Topp, 2015).

In this issue, Li et al. (2018) address the limitations in morphological evaluation with an innovative mathematical framework using a tool from the field of topological data analysis called persistent homology (PH) that can more accurately quantify phenotypic variation than other quantitative methods. In PH, topological features are monitored at different spatial resolutions to allow for traits or characters to be identified during analysis rather than prior to measurement. PH measurements can be designed to be orientation-independent and resistant to the noise that often accompanies data collection from two-dimensional (2D) images. In this way, PH captures multiple and comprehensive measurements better than uni- or multivariate systems because it constructs a single metric value from several morphological features. The PH metrics therefore capture more information about plant morphology in a comprehensive way than a single trait, and are not reliant on orientation or size, which is a significant factor in the ability of PH to integrate multiple morphological traits into a single descriptor that can be applied to different tissue types, growth conditions, and plant species.