MtreeRing: An R package with graphical user interface for automatic measurement of tree ring widths using image processing techniques

• Published in: Dendrochronologia (Verona) 2019-12, Vol.58, p.125644, Article 125644
• Main Authors: Shi, Jingning, Xiang, Wei, Liu, Qijing, Shah, Sher
• Format: Article
• Language: English
• Subjects: Automatic measurement; Graphical user interface (GUI); R package; Tree ring width
• ISSN: 1125-7865; 1612-0051
• DOI: 10.1016/j.dendro.2019.125644

Accurate measurements of ring-width series are essential for dendrochronological analyses. We present an R package MtreeRing for ring-width measurements on scanned digital images. A morphological alternate sequential filter is used for noise reduction in the original image. Ring boundaries are determined by the steepest negative slopes in the light reflectance of latewood-earlywood transitions. To automatically identify tree rings, the package provides three alternative methods (watershed-based segmentation, Canny edge detector, and a linear detection algorithm), each with advantages and disadvantages and suited to different wood anatomical features. The user can also manually mark tree rings on species with complex anatomical structures. The arcs of inner-rings and angles of successive inclined ring boundaries are used to correct ring-width series. Differences in ring-width measurements between MtreeRing and WinDENDRO in a given coniferous species (Larix gmelinii) were assessed, and no significant difference between programs was found. Furthermore, the package provides an R-based web application which was developed using the Shiny framework. This beginner-friendly application allows viewing and interacting with tree ring images. It requires no programming experience and can run on either a local computer or a remote server.