measuRing: An R package to measure tree-ring widths from scanned images

Lara, Wilson; Bravo, Felipe; Sierra, Carlos

doi:10.1016/j.dendro.2015.04.002

Cited by 34 publications

(17 citation statements)

References 25 publications

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“…All cores were mounted, sanded till tree-ring boundaries were clearly visible and scanned at 1800 ppi image resolution. For each cored tree, tree ring widths (mm year −1 ) were dated and measured from the scanned images using the 'measuRing' package (Lara et al, 2015). The quality of cross-dating and synchronization of the growth series were assessed using the 'dplR' package (Bunn, 2010).…”

Section: Field Site and Study Designmentioning

confidence: 99%

Changes in structural heterogeneity and stand productivity by mixing Scots pine and Maritime pine

Riofrío

Rı́o

Pretzsch

et al. 2017

Forest Ecology and Management

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Mixed-species stands have been studied extensively due to their potentially superior productivity, multi-functionality benefits and high ecological value compared to pure stands. The higher structural heterogeneity in mixed stands that can emerge from species interactions could be linked to the relationship between species diversity and ecosystem functions. We tested whether changes in stand structure also occur in mixtures of species with similar traits and whether they explain over-yielding patterns. Based on research with 12 triplets of Scots pine (Pinus sylvestris L.) and Maritime pine (Pinus pinaster Ait.) in the northern Iberian Peninsula (Spain), we provide evidence that species mixing increased structural heterogeneity and may induce over-yielding in mixed-species stands compared to monospecific stands. In this mixture of two light-demanding species, we observed that (i) stand composition influenced the inter-specific crown allometric variation, (ii) structural heterogeneity in mixed stands was caused by both specie-specific traits and species interactions, and (iii) intraspecific and interspecific differences in both crown size plasticity and size-distribution differentiation were associated with the increased relative productivity of mixed stands. We detected that crown complementarity and vertical stratification in the canopy space is a crucial mechanism for enhancing ecosystem productivity in light-demanding species and could be related to light interception and light-use. This work improves our understanding of emerging properties in mixed stands and introduces considerations for properly scaling and tracing mixing effects at individual tree, size distribution and stand levels.

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Section: Field Site and Study Designmentioning

confidence: 99%

Changes in structural heterogeneity and stand productivity by mixing Scots pine and Maritime pine

Riofrío

Rı́o

Pretzsch

et al. 2017

Forest Ecology and Management

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“…It can also be useful for methods that need to know the angle of the growth rings to generate an input image with a specific position, such as that proposed by Lara et al (Lara et al 2015), or to estimate the distance among rings, such as in the work of Van den Bulcke et al (Van den Bulcke et al 2014). The method presented in this article was evaluated employing Quercus petraea wood, which is that used to build barrels for the ageing of wines in cooperage.…”

Section: Results Comparison and General Analysismentioning

confidence: 99%

“…On the one hand, this angle will be useful for several semi-automated methods that need the user to introduce a path, because it will allow the process of generating this path to be automated. Some examples of this methods are those proposed by Hietz (Hietz 2011) or the methods implemented by WinDENDRO or CooRecorder.. On the other hand, the estimated angle will be useful for methods like that designed by Lara et al (Lara et al 2015), which needs to have the growth rings in a vertical or horizontal orientation It is interesting to note that the proposed method is able to align the growth rings in a vertical position, which is equivalent to estimating the angle of the linear path that perpendicularly crosses the growth rings, even in the pieces of wood with a significant estimation error. For example, Fig.…”

Section: Real Oak Wood Medullar Ray Angle Measurements and Estimationmentioning

confidence: 99%

“…This software analyses images to make its estimations but requires human assistance to prepare the samples and provide it with some information about these images. Another example is the work of Lara et al, which U V a M O X created a package in R statistical software (R Core Team) to measure tree-ring widths and identify ring borders from scanned images of wood (Lara et al 2015). This software allowed automatic detection of the features considered, but still requires time-consuming sample preparation involving human assistance.…”

Section: Introductionmentioning

confidence: 99%

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Method to estimate the medullar rays angle in pieces of wood based on tree-ring structure: application to planks of Quercus petraea

et al. 2017

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Estimating wood parameters employing non-destructive methods has been widely studied in recent years. The choice of wood used to build wine ageing barrels (cooperage) is strongly influenced by wood anatomy and specifically by the orientation of medullar rays among other aspects. In this article, a method based on the regularities of the tree-ring structure to estimate the medullar ray angle of the cross-section of a piece of wood is proposed. This angle shows the direction of the best linear path to evaluate several tree-ring features and could be employed to automate tasks, such as introducing an analysis path or rotating the image before the analysis, which some dendro analysis methods require. A dataset of 26992 synthetic images and 110 real oak wood images was used to validate the approach. The medullar ray angle of each image considered was measured manually and estimated using the method proposed here, which employs the Fast Fourier Transform (FFT) to take advantage of the tree-ring structure regularities and find the direction angle of the best linear path to evaluate several tree-ring features. The results obtained demonstrate a mean squared error of 0.29º and 8.19º and a mean absolute error of 0.19º and a 5.91º for the synthetic and oak wood images, respectively. These data suggest the suitability of the proposed method as part of an automated system to inspect and analyse the growth rings in oak wood planks.

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“…The BIOdry package can interact with other dendrochronological libraries in R, including dplR, bootRes, and measuRing 15 (Bunn, 2008;Lara et al, 2015;Zang and Biondi, 2013). For instance, the shiftFrame() function in the BIOdry package can format MEDS chronologies into dplR chronologies, and vice versa (R-code 1).…”

mentioning

confidence: 99%

R-Package <tt>BIOdry</tt>: DendroClimatic Modeling from Multilevel Ecological Data Series

Lara¹,

Bogino

Bravo³

2017

Preprint

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Abstract. R-package BIOdry is developed to consider ecological factors in dendroclimatic modeling of forest ecosystems.The package processes Multilevel Ecological Data Series (MEDS) with two functions: modelFrame() and muleMan().These integrate techniques for modeling Tree Rings in Wood (TRW) chronologies and climatic series at specific ecologicalfactor levels (one-level modeling), developing multilevel analysis (mixed-effects detrending), and implementing multivariate comparison of MEDS. Several one-level functions for serial synchronization, drought modeling and allometric scaling are Finally, enhancements in dendroclimatic modeling by accounting for ecological factors are tested. We conclude that BIOdry package is an useful tool for studying complex ecological time-space relationships.

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measuRing: An R package to measure tree-ring widths from scanned images

Cited by 34 publications

References 25 publications

Changes in structural heterogeneity and stand productivity by mixing Scots pine and Maritime pine

Changes in structural heterogeneity and stand productivity by mixing Scots pine and Maritime pine

Method to estimate the medullar rays angle in pieces of wood based on tree-ring structure: application to planks of Quercus petraea

R-Package <tt>BIOdry</tt>: DendroClimatic Modeling from Multilevel Ecological Data Series

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measuRing: An R package to measure tree-ring widths from scanned images

Cited by 34 publications

References 25 publications

Changes in structural heterogeneity and stand productivity by mixing Scots pine and Maritime pine

Changes in structural heterogeneity and stand productivity by mixing Scots pine and Maritime pine

Method to estimate the medullar rays angle in pieces of wood based on tree-ring structure: application to planks of Quercus petraea

R-Package &lt;tt&gt;BIOdry&lt;/tt&gt;: DendroClimatic Modeling from Multilevel Ecological Data Series

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R-Package <tt>BIOdry</tt>: DendroClimatic Modeling from Multilevel Ecological Data Series