A New Method for Counting Reproductive Structures in Digitized Herbarium Specimens Using Mask R-CNN

• Published in: Frontiers in plant science Vol. 11; p. 1129
• Main Authors: Davis, Charles C., Champ, Julien, Park, Daniel S., Breckheimer, Ian, Lyra, Goia M., Xie, Junxi, Joly, Alexis, Tarapore, Dharmesh, Ellison, Aaron M., Bonnet, Pierre
• Format: Journal Article
• Language: English
• Published: Frontiers 31.07.2020; Frontiers Media S.A
• Subjects: automated regional segmentation; Biodiversity; Biodiversity and Ecology; Botanics; deep learning; digitized herbarium specimen; Ecology, environment; Ecosystems; Environmental Sciences; Life Sciences; plant phenology; Plant Science; regional convolutional neural network; reproductive structures; Systematics, Phylogenetics and taxonomy; Vegetal Biology; Deep learning; Regional convolutional neural network; Digitized herbarium specimen; Visual data classification; Reproductive structures; Automated regional segmentation; Plant phenology
• ISSN: 1664-462X; 1664-462X
• DOI: 10.3389/fpls.2020.01129

Phenology—the timing of life-history events—is a key trait for understanding responses of organisms to climate. The digitization and online mobilization of herbarium specimens is rapidly advancing our understanding of plant phenological response to climate and climatic change. The current practice of manually harvesting data from individual specimens, however, greatly restricts our ability to scale-up data collection. Recent investigations have demonstrated that machine-learning approaches can facilitate this effort. However, present attempts have focused largely on simplistic binary coding of reproductive phenology (e.g., presence/absence of flowers). Here, we use crowd-sourced phenological data of buds, flowers, and fruits from >3,000 specimens of six common wildflower species of the eastern United States (Anemone canadensis L., A. hepatica L., A. quinquefolia L., Trillium erectum L., T. grandiflorum (Michx.) Salisb., and T. undulatum Wild.) to train models using Mask R-CNN to segment and count phenological features. A single global model was able to automate the binary coding of each of the three reproductive stages with >87% accuracy. We also successfully estimated the relative abundance of each reproductive structure on a specimen with ≥90% accuracy. Precise counting of features was also successful, but accuracy varied with phenological stage and taxon. Specifically, counting flowers was significantly less accurate than buds or fruits likely due to their morphological variability on pressed specimens. Moreover, our Mask R-CNN model provided more reliable data than non-expert crowd-sourcers but not botanical experts, highlighting the importance of high-quality human training data. Finally, we also demonstrated the transferability of our model to automated phenophase detection and counting of the three Trillium species, which have large and conspicuously-shaped reproductive organs. These results highlight the promise of our two-phase crowd-sourcing and machine-learning pipeline to segment and count reproductive features of herbarium specimens, thus providing high-quality data with which to investigate plant responses to ongoing climatic change.