Dr. Anne Bonnin


Beamline Scientist
TOMCAT Beamline

Paul Scherrer Institute
Forschungsstrasse 111
5232 Villigen PSI

Specialized in X-ray imaging (micro and nano-tomography, single-distance phase-retrieval) and powder diffraction (XRD-CT), my research interest focuses on developing new imaging methods to characterize materials and understand their behavior.

Since 2014, I am in charge of the TOMCAT nanoscope. This full field imaging setup allows to get a spatial resolution around 150 nm between 10-18 keV on sample of 50µm2. The setup can be used for absorption or phase contrast imaging. In this case, Zernike phase contrast is exploit to enhance contrast for phase objects.

As local contact, I collaborate with international researchers material sciences related (e.g. nuclear materials, explosives identification, cement hydration , ...) as well as paleontology (hominid dental microstructure , fossil as rock slabs) and biomedical applications (cardiac tissue imaging).

Since 2016, I lead the Heart Imaging Project. The main goal of this international project is to quantify the cardiac macro and micro-structure using synchrotron based X-ray Phase Contrast Imaging (X-PCI). We aim at providing new insights of the cardiac morphology at micrometre scale, non-destructively, without the use of contrast agents and in 3D. With the high resolution provided by X-PCI, we can have access for instance on the myofibres arrangement, vessels and trabeculation organization, and how they change with disease. Those informations are crucial for future clinical applications, not only to understand heart remodelling and the different patterns in cardiovascular disease, but also to provide more personalized and adapted treatments. For this purpose, we are developing dedicated acquisition methodology but also new analysis techniques based on Machine Learning algorithms.
During my PhD at the INSA de Lyon (France), I studied the physical properties of materials in order to discriminate explosive to common materials (see my PhD here). Then, I spent four years in the X-ray imaging group at the European Synchrotron Radiation Facility (Grenoble, France) where I gained experience in X-ray diffraction and X-ray phase contrast tomography. In April 2014, I joined the X-ray Tomography Group at PSI as post-doc in the Phase Contrast core of the CIBM (EPFL). Since January 2016, I am Beamline Scientist Tenure Track at the TOMCAT Beamline.

See also my Linkedin Profile.

An up-to-date publication list can be found here or in my orcid account https://orcid.org/0000-0001-5537-8682

  • Dejea H, Garcia-Canadilla P, Cook AC, Guasch E, Zamora M, Crispi F, et al.
    Comprehensive analysis of animal models of cardiovascular disease using multiscale X-ray phase contrast tomography
    Scientific Reports. 2019; 9(1): 6996 (12 pp.). https://doi.org/10.1038/s41598-019-43407-z
  • Dejea H, Tanner C, Achanta R, Stampanoni M, Perez-Cruz F, Konukoglu E, et al.
    Synchrotron X-ray phase contrast imaging and deep neural networks for cardiac collagen quantification in hypertensive rat model
    In: Coudière Y, Ozenne V, Vigmond E, Zemzemi N, eds. Funtcional imgaing and modeling of the heart. 10th international conference, FIMH 2019, Bordeaux, France, June 6-8, 2019, Proceedings. Vol. 11504. Lecture notes in computer science. Cham: Springer; 2019. https://doi.org/10.1007/978-3-030-21949-9_21
  • Garcia-Canadilla P, de Vries T, Gonzalez-Tendero A, Bonnin A, Gratacos E, Crispi F, et al.
    Structural coronary artery remodelling in the rabbit fetus as a result of intrauterine growth restriction
    PLoS One. 2019; 14(6): e0218192 (14 pp.). https://doi.org/10.1371/journal.pone.0218192
  • Miettinen A, Oikonomidis IV, Bonnin A, Stampanoni M
    NRStitcher: non-rigid stitching of terapixel-scale volumetric images
    Bioinformatics. 2019: btz423 (20 pp.). https://doi.org/10.1093/bioinformatics/btz423
  • Rücker M, Bartels W-B, Singh K, Brussee N, Coorn A, van der Linde HA, et al.
    The effect of mixed wettability on pore scale flow regimes based on a flooding experiment in Ketton limestone
    Geophysical Research Letters. 2019; 46(6): 3225-3234. https://doi.org/10.1029/2018GL081784
  • Unsal E, Rücker M, Berg S, Bartels WB, Bonnin A
    Imaging of compositional gradients during in situ emulsification using X-ray micro-tomography
    Journal of Colloid and Interface Science. 2019; 550: 159-169. https://doi.org/10.1016/j.jcis.2019.04.068
  • Wakonig K, Diaz A, Bonnin A, Stampanoni M, Bergamaschi A, Ihli J, et al.
    X-ray Fourier ptychography
    Science Advances. 2019; 5(2): eaav0282 (6 pp.). https://doi.org/10.1126/sciadv.aav0282
  • Wakonig K, Diaz A, Chiriotti S, Bergamaschi A, Bonnin A, Stampanoni M, et al.
    X-ray Fourier ptychography for out-of-focus measurements
    In: Lai B, Somogyi A, eds. X-ray nanoimaging: instruments and methods IV. Vol. 11112. Proceedings of SPIE. Bellingham, WA: SPIE; 2019. https://doi.org/10.1117/12.2528905
  • Garcia-Canadilla P, Dejea H, Bonnin A, Balicevic V, Loncaric S, Zhang C, et al.
    Complex congenital heart disease associated with disordered myocardial architecture in a midtrimester human fetus
    Circulation: Cardiovascular Imaging. 2018; 11(10): e007753 (10 pp.). https://doi.org/10.1161/CIRCIMAGING.118.007753
  • Krasnoshlyk V, Rolland Du Roscoat S, Dumont PJJ, Isaksson P, Ando E, Bonnin A
    Three-dimensional visualization and quantification of the fracture mechanisms in sparse fibre networks using multiscale X-ray microtomography
    Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. 2018; 474(2215): 20180175. https://doi.org/10.1098/rspa.2018.0175
  • Mokhtari M, Le Bourlot C, Adrien J, Bonnin A, Wada T, Duchet-Rumeau J, et al.
    Microstructure characterization by X-ray tomography and EBSD of porous FeCr produced by liquid metal dealloying
    Materials Characterization. 2018; 144: 166-172. https://doi.org/10.1016/j.matchar.2018.06.032
  • Bartels WB, Rücker M, Berg S, Mahani H, Georgiadis A, Fadili A, et al.
    Fast X-ray micro-CT study of the impact of brine salinity on the pore-scale fluid distribution during waterflooding
    Petrophysics. 2017; 58(1): 36-47.
  • Dejea H, Garcia-Canadilla P, Stampanoni M, Zamora M, Crispi F, Bijnens B, et al.
    Microstructural analysis of cardiac endomyocardial biopsies with synchrotron radiation-based X-ray phase contrast imaging
    In: Pop M, Wright GA, eds. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol. 10263 LNCS. FIMH: International Conference on Functional Imaging and Modeling of the Heart. Springer Verlag; 2017. https://doi.org/10.1007/978-3-319-59448-4_3
  • Etiemble A, Besnard N, Bonnin A, Adrien J, Douillard T, Tran-Van P, et al.
    Multiscale morphological characterization of process induced heterogeneities in blended positive electrodes for lithium–ion batteries
    Journal of Materials Science. 2017; 52(7): 3576-3596. https://doi.org/10.1007/s10853-016-0374-x
  • Ferreira Sanchez D, Simionovici AS, Lemelle L, Cuartero V, Mathon O, Pascarelli S, et al.
    2D/3D microanalysis by energy dispersive X-ray absorption spectroscopy tomography
    Scientific Reports. 2017; 7: 16453 (12 pp.). https://doi.org/10.1038/s41598-017-16345-x
  • Garcia-Canadilla P, Dejea i., Stampanoni M, Bijnens B, Bonnin A
    P1740Detailed characterization of myocardial infarct remodelling in rats by synchrotron x-ray phase-contrast imaging
    European Heart Journal. 2017; 38: 1. https://doi.org/10.1093/eurheartj/ehx502.P1740
  • Vanpeene V, Etiemble A, Bonnin A, Maire E, Roué L
    In-situ X-ray tomographic study of the morphological changes of a Si/C paper anode for Li-ion batteries
    Journal of Power Sources. 2017; 350: 18-27. https://doi.org/10.1016/j.jpowsour.2017.03.044