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Advanced X-ray CT scanning can boost tree-ring research for earth-system sciences

(2019) ANNALS OF BOTANY. 124(5). p.837-847
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Abstract
Background and Aims: Tree rings, as archives of the past and biosensors of the present, offer unique opportunities to study influences of the fluctuating environment over decades to centuries. As such, tree-ring-based wood traits are capital input for global vegetation models. To contribute to earth system sciences, however, sufficient spatial coverage is required of detailed individual-based measurements, necessitating large amounts of data. X-ray computed tomography (CT) scanning is one of the few techniques that can deliver such data sets. Methods: Increment cores of four different temperate tree species were scanned with a state-of-the-art X-ray CT system at resolutions ranging from 60 mu m down to 4.5 mu m, with an additional scan at a resolution of 0.8 mu m of a splinter-sized sample using a second X-ray CT system to highlight the potential of cell-level scanning. Calibration-free densitometry, based on full scanner simulation of a third X-ray CT system, is illustrated on increment cores of a tropical tree species. Key Results: We show how multiscale scanning offers unprecedented potential for mapping tree rings and wood traits without sample manipulation and with limited operator intervention. Custom-designed sample holders enable simultaneous scanning of multiple increment cores at resolutions sufficient for tree ring analysis and densitometry as well as single core scanning enabling quantitative wood anatomy, thereby approaching the conventional thin section approach. Standardized X-ray CT volumes are, furthermore, ideal input imagery for automated pipelines with neural-based learning for tree ring detection and measurements of wood traits. Conclusions: Advanced X-ray CT scanning for high-throughput processing of increment cores is within reach, generating pith-to-bark ring width series, density profiles and wood trait data. This would allow contribution to large-scale monitoring and modelling efforts with sufficient global coverage.
Keywords
X-ray CT, computed tomography, tree ring analysis, multiscale imaging, earth system sciences, increment cores, wood traits, densitometry, deep learning, scanner simulation, WOOD DENSITY, COMPUTED-TOMOGRAPHY, INCREMENT CORES, CONTRAST AGENTS, PHASE-RETRIEVAL, IMAGE, SOFTWARE, WIDTH, OAK, QUANTIFICATION

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Citation

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MLA
Van den Bulcke, Jan, et al. “Advanced X-Ray CT Scanning Can Boost Tree-Ring Research for Earth-System Sciences.” ANNALS OF BOTANY, vol. 124, no. 5, 2019, pp. 837–47, doi:10.1093/aob/mcz126.
APA
Van den Bulcke, J., Boone, M. A., Dhaene, J., Van Loo, D., Van Hoorebeke, L., Boone, M., … De Mil, T. (2019). Advanced X-ray CT scanning can boost tree-ring research for earth-system sciences. ANNALS OF BOTANY, 124(5), 837–847. https://doi.org/10.1093/aob/mcz126
Chicago author-date
Van den Bulcke, Jan, Marijn A Boone, Jelle Dhaene, Denis Van Loo, Luc Van Hoorebeke, Matthieu Boone, Francis wyffels, Hans Beeckman, Joris Van Acker, and Tom De Mil. 2019. “Advanced X-Ray CT Scanning Can Boost Tree-Ring Research for Earth-System Sciences.” ANNALS OF BOTANY 124 (5): 837–47. https://doi.org/10.1093/aob/mcz126.
Chicago author-date (all authors)
Van den Bulcke, Jan, Marijn A Boone, Jelle Dhaene, Denis Van Loo, Luc Van Hoorebeke, Matthieu Boone, Francis wyffels, Hans Beeckman, Joris Van Acker, and Tom De Mil. 2019. “Advanced X-Ray CT Scanning Can Boost Tree-Ring Research for Earth-System Sciences.” ANNALS OF BOTANY 124 (5): 837–847. doi:10.1093/aob/mcz126.
Vancouver
1.
Van den Bulcke J, Boone MA, Dhaene J, Van Loo D, Van Hoorebeke L, Boone M, et al. Advanced X-ray CT scanning can boost tree-ring research for earth-system sciences. ANNALS OF BOTANY. 2019;124(5):837–47.
IEEE
[1]
J. Van den Bulcke et al., “Advanced X-ray CT scanning can boost tree-ring research for earth-system sciences,” ANNALS OF BOTANY, vol. 124, no. 5, pp. 837–847, 2019.
@article{8627088,
  abstract     = {{Background and Aims: Tree rings, as archives of the past and biosensors of the present, offer unique opportunities to study influences of the fluctuating environment over decades to centuries. As such, tree-ring-based wood traits are capital input for global vegetation models. To contribute to earth system sciences, however, sufficient spatial coverage is required of detailed individual-based measurements, necessitating large amounts of data. X-ray computed tomography (CT) scanning is one of the few techniques that can deliver such data sets. 
Methods: Increment cores of four different temperate tree species were scanned with a state-of-the-art X-ray CT system at resolutions ranging from 60 mu m down to 4.5 mu m, with an additional scan at a resolution of 0.8 mu m of a splinter-sized sample using a second X-ray CT system to highlight the potential of cell-level scanning. Calibration-free densitometry, based on full scanner simulation of a third X-ray CT system, is illustrated on increment cores of a tropical tree species. 
Key Results: We show how multiscale scanning offers unprecedented potential for mapping tree rings and wood traits without sample manipulation and with limited operator intervention. Custom-designed sample holders enable simultaneous scanning of multiple increment cores at resolutions sufficient for tree ring analysis and densitometry as well as single core scanning enabling quantitative wood anatomy, thereby approaching the conventional thin section approach. Standardized X-ray CT volumes are, furthermore, ideal input imagery for automated pipelines with neural-based learning for tree ring detection and measurements of wood traits. 
Conclusions: Advanced X-ray CT scanning for high-throughput processing of increment cores is within reach, generating pith-to-bark ring width series, density profiles and wood trait data. This would allow contribution to large-scale monitoring and modelling efforts with sufficient global coverage.}},
  author       = {{Van den Bulcke, Jan and Boone, Marijn A and Dhaene, Jelle and Van Loo, Denis and Van Hoorebeke, Luc and Boone, Matthieu and wyffels, Francis and Beeckman, Hans and Van Acker, Joris and De Mil, Tom}},
  issn         = {{0305-7364}},
  journal      = {{ANNALS OF BOTANY}},
  keywords     = {{X-ray CT,computed tomography,tree ring analysis,multiscale imaging,earth system sciences,increment cores,wood traits,densitometry,deep learning,scanner simulation,WOOD DENSITY,COMPUTED-TOMOGRAPHY,INCREMENT CORES,CONTRAST AGENTS,PHASE-RETRIEVAL,IMAGE,SOFTWARE,WIDTH,OAK,QUANTIFICATION}},
  language     = {{eng}},
  number       = {{5}},
  pages        = {{837--847}},
  title        = {{Advanced X-ray CT scanning can boost tree-ring research for earth-system sciences}},
  url          = {{http://dx.doi.org/10.1093/aob/mcz126}},
  volume       = {{124}},
  year         = {{2019}},
}

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