Automated extraction of seed morphological traits from images

• Published in: Methods in ecology and evolution Vol. 14; no. 7; pp. 1708 - 1718
• Main Authors: Dayrell, Roberta L. C., Ott, Tankred, Horrocks, Tom, Poschlod, Peter
• Format: Journal Article
• Language: English
• Published: London John Wiley & Sons, Inc 01.07.2023; Wiley
• Subjects: Automation; Classification; Colorimetry; Correlation coefficient; Correlation coefficients; Datasets; Deep learning; diaspores; high‐throughput phenotyping; Image acquisition; Image analysis; Image contrast; Image processing; image segmentation; interpretability; Line interfaces; morphological description; Morphology; Object recognition; Open source software; Phylogeny; Physical characteristics; Scanners; seed morphology; seed traits; Seeds; Signal classification; Software; Taxa; trait measurement; Workflow
• DOI: 10.1111/2041-210X.14127
• ISSN: 2041-210X

The description of biological objects, such as seeds, mainly relies on manual measurements of few characteristics, and on visual classification of structures, both of which can be subjective, error prone and time‐consuming. Image analysis tools offer means to address these shortcomings, but we currently lack a method capable of automatically handling seeds from different taxa with varying morphological attributes and obtaining interpretable results. Here, we provide a simple image acquisition and processing protocol and introduce Traitor, an open‐source software available as a command‐line interface (CLI), which automates the extraction of seed morphological traits from images. The workflow for trait extraction consists of scanning seeds against a high‐contrast background, correcting image colours, and analysing images with the software. Traitor is capable of processing hundreds of images of varied taxa simultaneously with just three commands, and without a need for training, manual fine‐tuning or thresholding. The software automatically detects each object in the image and extracts size measurements, traditional morphometric descriptors widely used by scientists and practitioners, standardised shape coordinates, and colorimetric measurements. The method was tested on a dataset comprising of 91,667 images of seeds from 1228 taxa. Traitor's extracted average length and width values closely matched the average manual measurements obtained from the same collection (concordance correlation coefficient of 0.98). Further, we used a large image dataset to demonstrate how Traitor's output can be used to obtain representative seed colours for taxa, determine the phylogenetic signal of seed colour, and build objective classification categories for shape with high levels of visual interpretability. Our approach increases productivity and allows for large‐scale analyses that would otherwise be unfeasible. Traitor enables the acquisition of data that are readily comparable across different taxa, opening new avenues to explore functional relevance of morphological traits and to advance on new tools for seed identification.