CaptuRING: A do‐it‐yourself tool for wood sample digitization

García‐Hidalgo, Miguel; García‐Pedrero, Ángel; Colón, Daniel; Sangüesa‐Barreda, Gabriel; García‐Cervigón, Ana I.; López‐Molina, Juan; Hernández‐Alonso, Héctor; Rozas, Vicente; Olano, José Miguel; Alonso‐Gómez, Víctor

doi:10.1111/2041-210x.13847

Cited by 12 publications

(5 citation statements)

References 20 publications

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“…H. Schweingruber, WSL, Birmensdorf, Switzerland). High resolution images of the core's surface were obtained using the CaptuRING device (García-Hidalgo et al, 2022). The images were used to properly cross-date the tree-ring series from these cores with the previously created master chronologies using CooRecorder 9.6 (Cybis Elektronik & Data AB).…”

Section: Estimation Of Intrinsic Water Use Efficiencymentioning

confidence: 99%

Water use efficiency and climate legacies dominate beech growth at its rear edge

et al. 2023

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Rear‐edge tree populations are experiencing a combination of higher temperatures and more intense droughts that might push individuals beyond their tolerance limits. This trend towards rising atmospheric [CO2] is concurrent with an increase in intrinsic water use efficiency (iWUE), which theoretically enhances photosynthesis and decrease evapotranspiration rates, consequently improving tree resistance to drought. However, it remains unclear whether iWUE is favouring tree growth under current climate conditions, particularly when climate and iWUE legacy effects are simultaneously considered. We evaluated this question with an extensive sampling along Iberian rear‐edge (dry) populations comprising four mountain ranges and two distinct altitudes. We simultaneously examined the effects of climate and iWUE on secondary growth using annually resolved basal area increments (BAIs) for the period 1901–2017. We used linear mixed models including second‐order autocorrelation and 1‐year legacy effects of iWUE and summer drought. BAI and iWUE increased across the studied period. iWUE increase was driven by changes in atmospheric CO2 concentration and water availability during the growing season. Climate and iWUE exerted direct and lagged effects on beech growth. Water availability during growing season was the main driver of tree growth, combining direct and indirect effects through its impact on iWUE. Legacy effects of water availability and iWUE were more important than growing season conditions. The net effect of iWUE shifted when lagged effects were considered, resulting in a net negative impact on tree growth. Synthesis: Our results reveal that climate and iWUE legacy effects must be considered to assess the net iWUE effect on secondary growth. Considering lagged effects, the current increase in iWUE is constraining tree growth. Modelling efforts of tree growth response to climate warming should include climate and iWUE legacy effects to adequately assess terrestrial ecosystem carbon balance.

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Section: Estimation Of Intrinsic Water Use Efficiencymentioning

confidence: 99%

Water use efficiency and climate legacies dominate beech growth at its rear edge

et al. 2023

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“…Wood cores were air-dried, glued on wooden mounts, and polished with sandpaper of successively finer grain until the xylem cellular structure was clearly visible in transverse section. Afterwards, complete cores were digitized using the CaptuRING device, which automatically captures multiple images at a resolution of 5,931 dpi (García-Hidalgo et al, 2022). Images were merged using PTGUI v8.3.10 Pro (New House Internet Services B.V., Rotterdam, The Netherlands).…”

Section: Sampling and Dendrochronological Proceduresmentioning

confidence: 99%

Tree-ring distinctness, dating potential and climatic sensitivity of laurel forest tree species in Tenerife Island

et al. 2022

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“…The study of tree ring formation using dendrochronology involves a number of techniques to extract the information stored in the wood (Schweingruber, 1996). Recent technical advances in dendrochronological studies have improved data collection and processing using a wide range of tools, ranging from the traditional macroscopic to microscopic perspectives (von Arx et al, 2016;Garcia-Hidalgo et al, 2022). Initially, tree ring studies focused on observing wood samples using a stereoscopic set to determine total ring width and eventually early and latewood measurements, when this annual subdivision could be established, resulting in annually resolved time series of tree growth investment (Schweingruber et al, 2005).…”

Section: Introductionmentioning

confidence: 99%

Tree ring segmentation using UNEt TRansformer neural network on stained microsections for quantitative wood anatomy

García-Hidalgo,

García-Pedrero,

Rozas

et al. 2024

Front. Plant Sci.

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Forests are critical in the terrestrial carbon cycle, and the knowledge of their response to ongoing climate change will be crucial for determining future carbon fluxes and climate trajectories. In areas with contrasting seasons, trees form discrete annual rings that can be assigned to calendar years, allowing to extract valuable information about how trees respond to the environment. The anatomical structure of wood provides highly-resolved information about the reaction and adaptation of trees to climate. Quantitative wood anatomy helps to retrieve this information by measuring wood at the cellular level using high-resolution images of wood micro-sections. However, whereas large advances have been made in identifying cellular structures, obtaining meaningful cellular information is still hampered by the correct annual tree ring delimitation on the images. This is a time-consuming task that requires experienced operators to manually delimit ring boundaries. Classic methods of automatic segmentation based on pixel values are being replaced by new approaches using neural networks which are capable of distinguishing structures, even when demarcations require a high level of expertise. Although neural networks have been used for tree ring segmentation on macroscopic images of wood, the complexity of cell patterns in stained microsections of broadleaved species requires adaptive models to accurately accomplish this task. We present an automatic tree ring boundary delineation using neural networks on stained cross-sectional microsection images from beech cores. We trained a UNETR, a combined neural network of UNET and the attention mechanisms of Visual Transformers, to automatically segment annual ring boundaries. Its accuracy was evaluated considering discrepancies with manual segmentation and the consequences of disparity for the goals of quantitative wood anatomy analyses. In most cases (91.8%), automatic segmentation matched or improved manual segmentation, and the rate of vessels assignment to annual rings was similar between the two categories, even when manual segmentation was considered better. The application of convolutional neural networks-based models outperforms human operator segmentations when confronting ring boundary delimitation using specific parameters for quantitative wood anatomy analysis. Current advances on segmentation models may reduce the cost of massive and accurate data collection for quantitative wood anatomy.

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CaptuRING: A do‐it‐yourself tool for wood sample digitization

Cited by 12 publications

References 20 publications

Water use efficiency and climate legacies dominate beech growth at its rear edge

Water use efficiency and climate legacies dominate beech growth at its rear edge

Tree-ring distinctness, dating potential and climatic sensitivity of laurel forest tree species in Tenerife Island

Tree ring segmentation using UNEt TRansformer neural network on stained microsections for quantitative wood anatomy

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