Abstract
X-ray microtomography (μCT) is a three-dimensional imaging technique, which has, over the past decade, established itself as a go-to method for nondestructive visualization of plant tissue with submicrometer resolution. μCT is closely related to medical computed tomography, in that a measurement consists of acquiring a series of radiographs from different directions around the sample. Especially with synchrotron X-ray sources, these radiographs exhibit significant phase contrast. This greatly enhances soft tissue contrast, making it well suited for plant imaging. Tomographic reconstruction techniques are then employed to convert the stack of radiographs into a 3D volumetric image. Compared with the laboratory X-ray tube-based systems, synchrotron tomography beamlines also offer high throughput, with tens of samples scanned over the course of a typical 24-h beam time.
Synchrotrons are typically operated as user facilities, with a staff member assisting users in aligning the beamline and all instrumentation-related matters. From the user’s point of view, success of a synchrotron μCT experiment is often dependent on secure sample mounting, choice of appropriate beam parameters, and post-processing the data, i.e., extracting scientifically meaningful results from the 3D image. In this chapter, we review the issues to consider in preparation of a μCT experiment from the point of view of a phloem researcher, emphasizing those aspects which are directly under the user’s control rather than technical specifics, which vary from one beamline to another.
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References
Trtik P, Dual J, Keunecke D et al (2007) 3D imaging of microstructure of spruce wood. J Struct Biol 159:46–55
Derome D, Griffa M, Koebel M, Carmeliet J (2011) Hysteretic swelling of wood at cellular scale probed by phase-contrast X-ray tomography. J Struct Biol 173(1):180–190
Gilani MS, Boone MN, Mader K, Schwarze FWMR (2014) Synchrotron X-ray micro-tomography imaging and analysis of wood degraded by Physisporinus vitreus and Xylaria longipes. J Struct Biol 187:149–157
Holbrook NM, Zwieniecki MA (2005) Integration of long distance transport systems in plants: perspective and prospects for future research. In: Holbrook NM, Zwieniecki MA (eds) Vascular transport in plants. Physiological ecology series. Elsevier Academic Press, Cambridge, pp 537–545
Mullendore DL, Windt CW, Van As H, Knoblauch M (2010) Sieve tube geometry in relation to phloem flow. Plant Cell 22:579–593
Jyske T, Suuronen J-P, Pranovich A, Laakso T, Watanabe U, Kuroda K, Abe H (2015) Seasonal variation in formation, structure, and chemical properties of phloem in Picea abies as studied by novel microtechniques. Planta 242:613–629
Jyske T, Kuroda K, Suuronen J-P, Pranovich A, Roig Juan S, Aoki D, Fukushima K (2016) In planta localization of stilbenes within Picea abies phloem. Plant Physiol 172:913–928
Uggla C, Sundberg B (2002) Sampling of cambial region tissues for high resolution analysis. In: Chaffey N (ed) Wood formation in trees. Cell and molecular biology techniques. Taylor & Francis Inc, London, pp 215–228
Leroux O, Leroux F, Bellefroid E, Claeys M, Couvreur M, Borgonie G, Van Hoorebeke L, Masschaele B, Viane R (2009) A new preparation method to study fresh plant structures with X-ray computed tomography. J Microsc 233:1–4
Suuronen J-P, Peura M, Fagerstedt K, Serimaa R (2013) Visualizing water-filled vs embolized status of xylem conduits by desktop X-ray microtomography. Plant Methods 9:11
McElrone AJ, Choat B, Parkinson DY, MacDowell AA, Brodersen CR (2013) Using high resolution computed tomography to visualize the three dimensional structure and function of plant vasculature. J Vis Exp 74:50162. https://doi.org/10.3791/50162
Cochard H, Delzon S, Badel E (2015) X-ray microtomography (micro-CT): a reference technology for high-resolution quantification of xylem embolism in trees. Plant Cell Environ 38:201–206
Choat B, Brodersen CR, McElrone AJ (2015) Synchrotron X-ray microtomography of xylem embolism in Sequoia sempervirens saplings during cycles of drought and recovery. New Phytol 205:1095–1105. https://doi.org/10.1111/nph.13110
Leppänen K, Bjurhager I, Peura M, Kallonen A, Suuronen J-P, Penttilä P, Love J, Fagerstedt K, Serimaa R (2011) X-ray scattering and microtomography study on the structural changes of never-dried silver birch, European aspen and hybrid aspen during drying. Holzforschung 65:865–873
Paganin D, Mayo SC, Gureyev TE, Miller PR, Wilkins SW (2002) Simultaneous phase and amplitude extraction from a single defocused image of a homogeneous object. J Microsc 206:33–40
Mirone A, Brun E, Gouillart E, Tafforeau P, Kieffer J (2014) The PyHST hybrid distributed code for high speed tomographic reconstruction with iterative reconstruction and a priori knowledge capabilities. Nucl Instrum Methods Phys Res, Sect B 324:41–48
Martínez-Criado G, Villanova J, Tucoulou R, Salomon D, Suuronen J-P, Labouré S, Guilloud C, Valls V, Barrett R, Gagliardini E, Dabin Y, Baker R, Bohic S, Cohen C, Morse J (2016) ID16B: a hard X-ray nanoprobe beamline at the ESRF for nano-analysis. J Synchrotron Radiat 23:344–352
Cloetens P, Ludwig W, Baruchel J, Van Dyck D, Van Landuyt J, Guigay JP, Schlenker M (1999) Holotomography: quantitative phase tomography with micrometer resolution using hard synchrotron radiation X rays. Appl Phys Lett 75:2912
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Suuronen, JP., Jyske, T. (2019). Noninvasive Investigation of Phloem Structure by 3D Synchrotron X-Ray Microtomography. In: Liesche, J. (eds) Phloem. Methods in Molecular Biology, vol 2014. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9562-2_4
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DOI: https://doi.org/10.1007/978-1-4939-9562-2_4
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