CUTICLETRACE: A TOOLKIT FOR CAPTURING CELL OUTLINES OF LEAF CUTICLE WITH IMPLICATIONS FOR PALEOECOLOGY AND PALEOCLIMATOLOGY

The accurate and efficient characterization of the leaf epidermis is vital to disentangling the relationships between plant morphology, evolutionary history, and growth environment. Epidermal cells form the surface through which light capture and gas exchange takes place, serving as the primary interface between plants and their environment. Epidermal pavement cells exhibit highly variable morphology, influenced by both phylogeny and environment. This variation is of interest to a broad range of plant biologists, including paleobotanists, systematists, and physiologists. Existing automated methods for epidermal pavement cell segmentation are limited in their application and have not been widely adopted. The labor needed to generate hand-traced datasets have circumscribed the use of epidermal cell morphology in paleoenvironmental, phylogenetic, and phenomic research. To streamline epidermal cell analysis, we developed CuticleTrace, a suite of FIJI and R-based functions that streamlines and automates the segmentation and measurement of epidermal pavement cells across a wide range of cell morphologies and image qualities. CuticleTrace results are comparable to expert hand-traced measurements and improve upon results generated by students and alternate automated methods. CuticleTrace is broadly applicable, modular, and customizable, and integrates data visualization and cell shape measurement with image segmentation, lowering the barrier to high-throughput studies of epidermal morphology.