Phloem pp 37-54 | Cite as

Noninvasive Investigation of Phloem Structure by 3D Synchrotron X-Ray Microtomography

  • Jussi-Petteri Suuronen
  • Tuula JyskeEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 2014)


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.

Key words

Axial parenchyma Cambium Microtomography Phloem Picea abies Ray parenchyma Sieve cells Synchrotron radiation Quantitative anatomy 


  1. 1.
    Trtik P, Dual J, Keunecke D et al (2007) 3D imaging of microstructure of spruce wood. J Struct Biol 159:46–55CrossRefGoogle Scholar
  2. 2.
    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):180–190CrossRefGoogle Scholar
  3. 3.
    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 187:149–157CrossRefGoogle Scholar
  4. 4.
    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 537–545CrossRefGoogle Scholar
  5. 5.
    Mullendore DL, Windt CW, Van As H, Knoblauch M (2010) Sieve tube geometry in relation to phloem flow. Plant Cell 22:579–593CrossRefGoogle Scholar
  6. 6.
    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 242:613–629CrossRefGoogle Scholar
  7. 7.
    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 172:913–928PubMedPubMedCentralGoogle Scholar
  8. 8.
    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 215–228CrossRefGoogle Scholar
  9. 9.
    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 233:1–4CrossRefGoogle Scholar
  10. 10.
    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 9:11CrossRefGoogle Scholar
  11. 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. Scholar
  12. 12.
    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 38:201–206CrossRefGoogle Scholar
  13. 13.
    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. Scholar
  14. 14.
    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 65:865–873CrossRefGoogle Scholar
  15. 15.
    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 206:33–40CrossRefGoogle Scholar
  16. 16.
    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 324:41–48CrossRefGoogle Scholar
  17. 17.
    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 23:344–352CrossRefGoogle Scholar
  18. 18.
    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 75:2912CrossRefGoogle Scholar

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© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.ESRF-The European SynchrotronGrenobleFrance
  2. 2.Production Systems, Biomass Characterization and PropertiesNatural Resources Institute Finland (Luke)EspooFinland

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