FoliometriK: application in R language for automated morphometric measurements of leaves using digital photography

• Main Authors: Víctor Manuel Ramírez-Arrieta, Dennis Denis Ávila
• Format: Article
• Language: English
• Published: Universidad de La Habana 2020-07-01
• Series: Revista del Jardín Botánico Nacional
• Subjects: análisis digital de imágenes; aplicación de r; automatización; morfología foliar
• Online Access: http://www.rjbn.uh.cu/index.php/RJBN/article/view/454
• ISSN: 0253-5696; 2410-5546

Foliar morphometric studies usually are limited by the need of processing many samples. That is why the process automation represents an advantage. We present FoliometriK as an open application integrated into an R app for obtaining automatic morphometric measurements of plant leaves using digital pictures and calibrated with a reference scale. The app allows obtaining eight primary lineal variables (blade area, perimeter, length, maximum width, the height of maximum width and width at three main axis percentile) and four angles (apical, basal and lateral). In basallobed leaves, other variables can be obtained: length from apex to top of the basal lobes, lobes depth, width at petiole, angle between lobes and relative lobes area. From these variables two relative indexes are calculated: a shape index and a lateral asymmetry index. For geometric morphometry analysis we also include principal component scores from contour Fourier descriptors and contour landmarks fixed by radial grid (at constant angles) or parallel grid (equally spaced). Algorithm for image processing and variable calculation was designed in a friendly HTML interface, integrated into an R app, and validated with a 40 leaves sample of Avicennia germinans (Avicenniaceae), obtained from field samples and manually measured, at the same time, with a Vernier caliper and in ImageJ. Differences among manual measures or by ImageJ tools and those obtained by using the R app were less than 3 %, but time of data gather and final variances were markedly reduced. We conclude that FoliometriK application permit to extract in a fast way, with precision and semi automatically a high variety of measurements from simple and relatively symmetric leaves, so it is expected that help to promote ecomorphological, taxonomic or phenotypic trait studies in natural populations. Citation: Ramírez-Arrieta, V.M. & Denis, D. 2020. FoliometriK: aplicación en lenguaje R para mediciones morfométricas automatizadas de hojas a partir de fotografías digitales. Revista Jard. Bot. Nac. Univ. Habana 41: 15-23. Article history: Received 18 March 2020. Accepted: 3 April 2020. Online: 3 June 2020. Editor: José Angel García-Beltrán.