CTRing: An R package to extract wood density profiles from computed tomography images of discs and logs

IF 2.7 3区 农林科学 Q1 FORESTRY
Dipak Mahatara , Filipe Campelo , Laurent Houle , Alain Caron , Julie Barrette , Pierre Francus , Robert Schneider
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引用次数: 0

Abstract

Accurately determining the position of pith and accessing tree-ring density profiles, including intra-ring variations, is important for both the forest industry and dendroclimatology. Although several available methods exist for acquiring this information, such as X-ray computed tomography (CT), micro-CT, and X-ray films, the availability of open-source programs for extracting data remains limited. The CTRing package in the R environment integrates a series of functions to detect precisely the pith and tree-ring boundaries and generate tree-ring density profiles using CT images of tree cross sections. Before processing, grey values are transformed into density using a calibration function. Pith position is then detected by combining an adapted Hough Transform method and a one-dimensional edge detector. Tree-ring profiles along the pith-to-bark path of interest are inspected visually, and tree-ring boundaries can be easily added or removed manually via a graphical user interface. After correcting for tree-ring boundaries, the inflection points of a 3rd-degree polynomial obtained from density profiles are used to delimit the earlywood–latewood transition. We tested this package using 60 CT-scanned images of white spruce (Picea glauca (Moench) Voss) discs collected at various tree heights (0 %, 25 %, 50 % and 75 % of the total tree height as well as at 1.3 m). The pith detection function had an average mean error of 0.72 mm with 95 % of the automatically detected pith locations that differed by less than 2 mm from their manually located positions. Error decreased toward the apex of the tree. The functions of the CTRing package are flexible and can be easily implemented or adapted. The package could also be used with simple images of discs to obtain ring-width time series; however, this use must be evaluated further. Future work with this package involves assessing the use of low-quality images and ring-porous species.
CTRing:从圆盘和原木的计算机断层扫描图像中提取木材密度剖面的 R 软件包
准确确定髓部位置和获取树环密度剖面,包括环内变化,对林业和树木气候学都很重要。虽然有多种可用的方法来获取这些信息,如 X 射线计算机断层扫描(CT)、显微 CT 和 X 射线胶片,但用于提取数据的开源程序仍然有限。R 环境中的 CTRing 软件包集成了一系列函数,可精确检测髓部和树环边界,并利用树木横截面的 CT 图像生成树环密度剖面图。处理前,使用校准函数将灰度值转换为密度。然后,结合改良的 Hough 变换方法和一维边缘检测器检测髓部位置。沿着感兴趣的髓部到树皮路径的树环剖面可通过视觉进行检查,树环边界可通过图形用户界面轻松手动添加或删除。校正树环边界后,利用从密度剖面获得的三度多项式的拐点来划定早材-晚材的过渡。我们使用在不同树高(总树高的 0%、25%、50% 和 75%,以及 1.3 米处)采集的 60 张白云杉(Picea glauca (Moench) Voss)圆盘 CT 扫描图像对该软件包进行了测试。髓部检测功能的平均误差为 0.72 毫米,95% 自动检测到的髓部位置与人工定位的位置相差不到 2 毫米。误差向树顶方向减小。CTRing 软件包的功能非常灵活,易于实施或调整。该软件包还可与简单的圆盘图像一起使用,以获得环宽时间序列;不过,这一用途还需进一步评估。该软件包的未来工作包括评估低质量图像和多孔环树种的使用情况。
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来源期刊
Dendrochronologia
Dendrochronologia FORESTRY-GEOGRAPHY, PHYSICAL
CiteScore
5.50
自引率
13.30%
发文量
82
审稿时长
22.8 weeks
期刊介绍: Dendrochronologia is a peer-reviewed international scholarly journal that presents high-quality research related to growth rings of woody plants, i.e., trees and shrubs, and the application of tree-ring studies. The areas covered by the journal include, but are not limited to: Archaeology Botany Climatology Ecology Forestry Geology Hydrology Original research articles, reviews, communications, technical notes and personal notes are considered for publication.
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