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,X-ray microtomography

X-ray microtomography at INRA Clermont-Ferrand

For more information, contact Eric BADEL (

What is X-ray microtomography?

X-ray microtomography is a non-destructive method that allows access to the inner vision of an object (composition, arrangement, defects, porosity); that is to say without cutting the sample. The use of this technique is currently experiencing a boom, particularly in biology.

This imaging technique is based on the property of X-rays to pass through the material and be absorbed in function of the nature and density of the components they cross. A tomographic scan consists in the recording a series of digital radiographs of the sample at various angles. After a "reconstruction" computation, these data allow the 3D visualization, mapping real variation of attenuation of X-rays through the object.


Aiguille de pin

Structure of a pine needle

Charra-Vaskou et al 2012

(Tree Physiology)

Distribution of summer embolism

in an annual ring of Douglas wood

Dalla-Salda et al 2014 (J Plant Hydraulics)

Therefore, the internal structure of the object can be described qualitatively and quantitatively:

  • Dimensional measurements in three dimensions
  • Spatial distribution of the various phases of a heterogeneous material.
  • Characterization of porosity (connectivity, etc)

Microtomograph "Nanotom" installed at INRA-Clermont-Ferrand

The characteristics of our Nanotom installed at INRA in Clermont Ferrand can cover samples from sub-millimeter to ten centimeters with spatial resolutions ranging from 1 to 50 microns.

The device consists of a model microtomograph "Nanotom" Phoenix GE company and a set of six work stations for the acquisition and processing of the 2D and 3D images.

Ensemble Nanotom
Interieur Nanotom

X-ray microtomography device at INRA Clermont-Ferrand

The sample room

Some characteristics of microtomograph "Nanotom" installed at INRA-Clermont-Ferrand (Crouël site):

  • An X-ray source-focus nano Phoenix GE (160kV, 15W, 0,9μm) equipped with interchangeable targets (tungsten or molybdenum) to pass through high density objects (metal, rocks, etc.) and for the adjustable scan of samples of low density as the original biological objects.
  • An imaging (2000 x 2000 pixels) of Hamamatsu 50 microns spatial resolution. Ability to create a virtual imaging to increase the field of view.
  • Reconstruction of the images on a cluster of four stations (32 GB RAM): 10003 voxels are reconstructed in few minutes
  • Spatial resolution from 50 microns to 0,9μm.
  • Maximum field of view: 80 mm.
  • Scan time from a few minutes to one hour.

Processing softwares and visualization of 2D and 3D images such as vgstudio, ImageJ, Matlab tools.

The PIAF applications

PIAF has developed particular expertise on the observation of biological objects and in particular on plants.

Few examples of observations: Hydraulic architecture and embolism of branches, tree stems, leaves, needles, starch in wheat grain, maize grain, biomimetic microfluidic circuit characterization, mouse bone structure.

Focus on our X tomography activities, in the news INRA website :

References :

Torres-Ruiz J.M., Cochard H., Mencuccini M., Delzon S., Badel E. 2016. Direct observation and modelling of embolism spread between xylem conduits: a case study in Scots pine. Plant Cell Environ. 39(12):2774-2785. doi: 10.1111/pce.1284

Dalla-Salda G., Fernández M.E., Sergent A.S., Rozenberg P., Badel E. and Martinez-Meier A. 2014. Dynamics of cavitation in a Douglas-fir tree-ring: transition-wood, the lord of the ring? JPH DOI:

Cochard H., Delzon S. and Badel E., 2014. X-ray microtomography (micro-CT): a reference technology for high-resolution quantification of xylem embolism in trees. PCE. doi: 10.1111/pce.12391

Dalla-Salda G., Fernández M.E., Sergent A.S., Rozenberg P., Badel E. and Martinez-Meier A. 2014. Dynamics of cavitation in a Douglas-fir tree-ring: transition-wood, the lord of the ring? JPH (in press)

Torres-Ruiz J.M., Cochard H., Mayr S., Beikircher B., Diaz-Espejo A., Rodriguez-Dominguez C.M., Badel E., Fernández J.E, 2014. Vulnerability to cavitation in Olea europaea current-year shoots: more support to the open-vessel artefact with centrifuge and air-injection techniques. Physiol Plantarum doi: 10.1111/ppl.12185

Charra-Vaskou K., Badel E., Burlett R., Cochard H., Delzon D., Mayr S., 2012. Hydraulic efficiency and safety of vascular and non-vascular components in Pinus pinaster leaves. Tree Physiol, 32 (9): 1161-1170


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