Photo Joseph Brunet portrait

About me

Hi, I'm Joseph Brunet, a Post-Doctoral Research Fellow in biomedical at University College London, based at European Synchrotron Radiation Facility (ESRF).

I am part of an international team which uses a new imaging technique called Hierarchical Phase contrast Computed Tomography (HiP-CT) to image whole human organs down to cellular level. This was enabled by the recent upgrade to the ESRF in Grenoble. We recently made fondamental discoveries in the mechanicsms behind COVID-19 effect on lung vasculature.

Curriculum vitae

I'm a curious mind, always looking for new experiences and problems to solve. This has led me to explore different fields like mechanics, biology or imaging, and combined them to open perspectives on the development of personalised diagnostic tools for patients.

Research

3D rendering of a heart

The Heart Atlas

Exploring the detailed structural features of the heart using Hierarchical Phase-Contrast Tomography (HiP-CT)

Cardiac Imaging
HiP-CT
Synchrotron X-ray Tomography

During my postdoc at the European Synchrotron Radiation Facility (ESRF) I used Hierarchical Phase-Contrast Tomography (HiP-CT) to depict the macro- to microanatomy of structurally normal and abnormal adult human hearts ex vivo. The study involved imaging two hearts: one from a healthy 63-year-old male and another from an 87-year-old female with multiple cardiovascular diseases. HiP-CT provided high-spatial-resolution, three-dimensional images revealing histologic-level details of the myocardium, valves, coronary arteries, and the cardiac conduction system without invasive sectioning or contrast agents.

Tension-inflation experiment at the synchrotron

Aortic dissection

Understanding the mechanisms of aortic dissection

Artic dissection
Tension-inflation
Synchrotron X-ray tomography

During my PhD, I worked at identifying and quantifying the mechanisms behind vascular failure and especially aortic dissection in order to develop new diagnostic tools and treatments for clinics. To this end, I performed in situ experiments combining mechanical testing and imaging techniques. I created an in vitro aortic dissection and I observed it with X-ray micro-tomography, using either laboratory or synchrotron X-ray sources. This approach made it possible to observe the 3D evolution of the delamination profile during the propagation of a dissection in the aortic wall. Inverse methods allowed me to quantify the elastic and failure properties of the aorta. Finilly, I used finite element models to model the rupture and investigate the fracture modes of the tissue.

Publications Icon research publication

You can also find my scientific publications on my Google Scholar profile.

2024

  • Brunet J., A. C. Cook, C. L. Walsh, J. Cranley, P. Tafforeau, K. Engel, C. Berruyer, E. Burke OLeary, A. Bellier, R. Torii, C. Werlein, D. D. Jonigk, M. Ackermann, K. Dollman, P. D. Lee. Multidimensional Analysis of the Adult Human Heart in Health and Disease using Hierarchical Phase-Contrast Tomography (HiP-CT). Radiology, 312(1). doi: 10.1148/radiol.232731. Cover of the July 2024 issue.

  • Mirone A., J. Brunet, R. Boistel, M. Sowinski, C. Berruyer, H. Payno, E. Boller, P. Paleo, C. L. Walsh, P. D. Lee, P. Tafforeau. Eikonal phase retrieval: Unleashing the fourth generation sources potential for enhanced propagation based tomography on biological samples. Preprint. doi: 10.48550/ARXIV.2311.14745

  • Yagis E., S. Aslani, Y. Jain, Y. Zhou, S. Rahmani, J. Brunet, A. Bellier, C. Werlein, M. Ackermann, D. Jonigk, P. Tafforeau, P. D. Lee, C. Walsh. Deep Learning for Vascular Segmentation and Applications in Phase Contrast Tomography Imaging. Preprint. doi: 10.48550/ARXIV.2311.13319

  • Xian R. P., Brunet J., Huang Y., Wagner L. W., Lee D. L., Tafforeau P., and Walsh L. C. A closer look at high-energy X-ray-induced bubble formation during soft tissue imaging. Synchrotron Radiation, 31(3), pp.566-577. doi: 10.1107/s160057752400290x. (Co-first author)

2023

  • Ackermann M., Tafforeau P., Brunet J., Kamp J. C., Werlein C., Khnel M. P., Jacob J. et al. Comment on: Intrapulmonary shunt and alveolar dead space in a cohort of patients with acute COVID-19 pneumonitis and early recovery. European Respiratory Journal, 61(2). doi: 10.1183/13993003.02121-2022

  • Brunet J., Walsh C. L., Wagner W. L., Bellier A., Werlein C., Marussi S., Jonigk D. D., Verleden E. S., Ackermann M., Lee D. P., Tafforeau P. Preparation of large biological samples for high-resolution, hierarchical, multi-modal imaging. Nature Protocols, 18, 1441-1461. doi: 10.1038/s41596-023-00804-z

2022

  • Brunet J., Pierrat B., Adrien J., Maire E., Lane B. A., Curt N., Bravin A., Laroche N., Badel P. In situ visualization of aortic dissection propagation in notched rabbit aorta using synchrotron X-ray tomography. Acta Biomaterialia, 155, pp.449-460. doi: 10.1016/j.actbio.2022.10.060

2021

  • Brunet J., Pierrat B., and Badel P. A parametric study on factors influencing the onset and propagation of aortic dissection using the extended finite element method. IEEE Transactions on Biomedical Engineering, 68(10), pp.2918-2929. doi: 10.1109/TBME.2021.3056022

  • Brunet J., Pierrat B., and Badel P. Review of current advances in the mechanical description and quantification of aortic dissection mechanisms. IEEE Reviews in Biomedical Engineering, 14, pp.240-255. doi: 10.1109/RBME.2019.2950140

2020

  • Brunet J., Pierrat B., Adrien J., Maire E., Curt N., and Badel P. A Novel Method for In Vitro 3D Imaging of Dissecting Pressurized Arterial Segments Using X-Ray Microtomography. Experimental Mechanics, 61, pp.147-157. doi: 10.1007/s11340-020-00645-x

2019

  • Brunet J., Pierrat B., Adrien J., Maire E., and Badel P. A combined experimental-numerical lamellar-scale approach of tensile rupture in arterial medial tissue using X-ray tomography. Journal of the mechanical behavior of biomedical materials, 95, pp.116-123. doi: 10.1016/j.jmbbm.2019.03.028

Conferences

2024

  • Big Data and Big Science Workshop (May 8)
    Oral presentation entitled: "Creating The Human Organ Atlas with HiP-CT", Johannesburg, South Africa.

  • XXVImes Journes Francophones de Virologie (April 11)
    Oral presentation entitled: "Human Organ Atlas project: High-resolution imaging of whole human organs and application on COVID-19", Brussels, Belgium.

2023

  • GDR CNRS FIBMAT (December 1)
    Oral presentation entitled: "In situ quantification of the mechanical behavior of arteries using synchrotron X-ray tomography", Lyon, France.

  • BioMedEng23 (September 14)
    Oral presentation entitled: "Hierarchical Phase-Contrast Tomography for High-Resolution imaging of Ex Vivo Whole Adult Human Heart in Health and Disease", Swansea, UK.

  • "High-resolution imaging in correlative workflows" Workshop organized by Zeiss at the Technical University of Munich (July 3)
    Key-lecture presentation entitled: "BM18, the new ESRF-EBS beamline for multiresolution phase-contrast tomography on large samples: past, present and future", Munich, Germany.

  • Ecole des Mines de Saint-Etienne Seminar (July 3)
    Seminar entitled: "X-ray imaging at BM18 - Human Organ atlas project", Saint-Etienne, France.

  • 6th Annual Workshop on Advances in X-ray imaging (June 22)
    Oral presentation entitled: "Imaging of whole human organs using Hierarchical Phase-Contrast Tomography (HiP-CT)", Harwell, UK.

  • 3D image analysis From Foundation to Vision Workshop at the Center for Quantification of Imaging Data from MAX IV (QIM) (March 10)
    Oral presentation entitled: "Human Organ Atlas project: Whole Human Organs Imaged in Synchrotrons", Copenhagen, Denmark.

2022

  • BioMedEng22 (September 14)
    Oral presentation entitled: "Hierarchical Phase-Contrast Tomography for High-Resolution imaging of Ex Vivo Whole Adult Human Heart in Health and Disease", Swansea, UK.

  • Witwatersrand University Seminar (September 6)
    Seminar entitled: "Imaging of whole human organs using Hierarchical Phase-Contrast Tomography (HiP-CT)", Johannesburg, South Africa.

  • 5th International Conference on Tomography of Materials and Structures (ICTMS) (July 25)
    Oral presentation entitled: "High-resolution imaging of the whole human heart using synchrotron x-ray tomography", Grenoble, France.

  • Science Day Symposium, ESRF (March 21)
    Oral presentation entitled: "Hierarchical imaging of complete human organs, how the EBS changed the game", ESRF, France.

2021

  • 26th Congress of the European Society of Biomechanics (ESBiomech2020) (July 11)
    Oral presentation delivered entitled: 3D characterization of crack propagation during the onset of a dissection using X-ray microtomography on pressurized aortic segments, Online.

  • 46th Congress of the Société de Biomécanique (October 25)
    Oral presentation delivered entitled: In situ observation of an in vitro aortic dissection in rabbit aortic tissue with synchrotron-based X-ray microtomography, Saint-Etienne, France.

2020

  • 45th Congress of the Société de Biomécanique (October 28)
    Oral presentation delivered entitled: Investigation of notch propagation in an in-vitro dissection model using X-ray microtomography, Online.

2019

  • 44th Congress of the Société de Biomécanique (October 30)

    Chairman of the session ”Macro-scale biofluids” and oral presentation delivered entitled: A numerical design of experiment approach to understand aortic dissection onset and propagation, Poitiers, France.

2018

  • 8th World Congress of Biomechanics (July 10)
    Poster presentation delivered entitled: A combined experimental-numerical meso-scale approach of tensile rupture in arterial medial tissue using X-ray tomography, Dublin, Ireland.

  • 15th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering (March 28)
    Oral presentation delivered entitled: Characterization and modelling of rupture in arterial medial tissue under tension from in situ experiments with X-ray tomography, Lisbon, Portugal.

Teaching

Co-Supervisor, ESRF/UCL (2021-2024)

  • Co-supervised MS and PhD students in projects related to mechanical testing, image processing and analysis, and deep learning

Training Provider, ESRF (2021-2024)

  • Provided training to PhD students and postdocs in sample preparation, scan acquisition, and image reconstruction

Teaching Assistant, Ecole des Mines de Saint-Etienne

  • Experimental mechanics

  • Finite element method

  • Supervisor of master students - Industrial and research projects