You can also follow my work on Google Scholar or ORCID.

Selected publications

Software

Cardiotensor: Orientation Analysis and Tractography in 3D Cardiac Imaging

J Brunet, L Chestnutt, M Chourrout, H Dejea, V Sabarigirivasan, PD Lee, AC Cook

Open-source, scalable analysis of myocardial organisation in large three-dimensional cardiac datasets.

Journal of Open Source Software · 2026

Paper ↗Code ↗Documentation ↗
Journal article

The Human Organ Atlas

CL Walsh, J Brunet

An open, multiscale three-dimensional atlas of intact human organs acquired with HiP-CT.

Science Advances · 2026

Paper ↗
Journal article

Multidimensional analysis of the adult human heart in health and disease using HiP-CT

J Brunet

Whole-heart imaging that connects organ-scale anatomy with near-cellular cardiac microstructure.

Radiology · 2024

Paper ↗Research story →
Protocol

Preparation of large biological samples for hierarchical synchrotron tomography

J Brunet

A reproducible preparation workflow for high-resolution, multimodal HiP-CT imaging of intact organs.

Nature Protocols · 2023

Paper ↗

Full publication list

202618 publications
Preprint

LoRCA: LoRA Cycle Adaptation for Histology to HiP-CT Translation with DINOv3

Y Zhou, E Occhipinti, BK Elvis, J Chen, S Megas, J Brunet

arXiv preprint (2026). Preprint

Preprint

Multimodal Hypersampling of the adult human heart resolves tissue-specific cell states and disease-associated variants

J Cranley, L Mach, T Jimba, K Kanemaru, J Zhao, S Perera, YX Zurke, S Koplev, S Barnett, L Wang, et al.

bioRxiv preprint (2026). Preprint

Journal article

In Situ Profiling of Nanoscale Strains Uncovers Mechano-Architectural Predictors of Aging and Osteoarthritis Emergence

A Sharma, LAE Evans, LE Bourne, J Chen, AL Parmenter, J Brunet

Advanced Science (2026). Paper

Journal article

Unravelling the Enigmatic Morphology of the Atrioventricular Conduction Axis Using Hierarchical Phase-Contrast Tomography (HiP-CT)

A Almehandi, KYC Li, J Brunet, PD Lee, RH Anderson, AC Cook

Heart Rhythm, in press (2026). Paper

Journal article

Fast Eikonal Phase Retrieval for High-Throughput Beamlines

A Mirone, T Urban, J Brunet, CL Walsh, PD Lee, P Tafforeau

Journal of Synchrotron Radiation 33(4), 1169–1179 (2026). Paper

Journal article

Vasculature segmentation in 3D hierarchical phase-contrast tomography images of human kidneys

Y Jain, CL Walsh, E Yagis, S Aslani, S Nandanwar, Y Zhou, J Ha, KS Gustilo, J Brunet

Nature Communications (2026). Paper

Journal article

Evolution of Hierarchical Phase-Contrast Tomography on the European Synchrotron Beamlines BM05 and BM18: A Whole Adult Human Brain Imaging Case Study

H Dejea†, J Brunet†, T Urban, C Berruyer, A Mirone, C Jarnias, A Bellier, CL Walsh, PD Lee, P Tafforeau

Journal of Synchrotron Radiation 33(4), 1180–1189 (2026). Paper

Journal article

The heterogeneous nature of atrioventricular conduction tissues in tetralogy of Fallot demonstrated by hierarchical phase-contrast tomography

V Sabarigirivasan, J Brunet

JTCVS Structural and Endovascular 10, 100111 (2026). Paper

Software

Cardiotensor: A Python Library for Orientation Analysis and Tractography in 3D Cardiac Imaging

J Brunet, L Chestnutt, M Chourrout, H Dejea, V Sabarigirivasan, PD Lee, AC Cook

Journal of Open Source Software 11(121), 9720 (2026). Paper

Preprint

Altered Myocardial Structure in Post-natal Tetralogy of Fallot: A Substrate for Interpretation of Ventricular Function and Dysfunction?

V Sabarigirivasan, J Brunet

bioRxiv preprint (2026). Preprint

Journal article

The Human Organ Atlas

CL Walsh, J Brunet

Science Advances 12(11) (2026). Paper

Preprint

Bridging the microstructural gap in human connectomics using hierarchical phase-contrast tomography as a reference for diffusion MRI in the human brain

E Wanjau, M Chourrout, C Maffei, Y Balbastre, A Keenlyside, J Brunet

bioRxiv preprint (2026). Preprint

Preprint

Hierarchical X-ray microscopy and mesoscopic diffusion MRI in the same brain reveal the human connectome across scales

M Chourrout, T Gong, R Schalek, A Keenlyside, Y Balbastre, N Karlupia, RA Gonzales, IN Huszar, E Wanjau, J Brunet

bioRxiv preprint (2026). Preprint

Preprint

Neuroanatomy of the clitoris

JY Lee, D Alblas, A Szmul, D Docter, H Dejea, Y Dawood, J Hanemaaijer-van der Veer, A Bellier, T Urban, J Brunet

bioRxiv preprint (2026). Preprint

Preprint

The Extremely Brilliant Brain: An Isotropic Microscale Human Brain Dataset

M Chourrout, A Keenlyside, E Wanjau, Y Balbastre, E Yagis, J Brunet

bioRxiv preprint (2026). Preprint

Preprint

Hierarchical Phase-Contrast Tomography Imaging: Applicability in biomedical research

D Docter, J Brunet

bioRxiv preprint (2026). Preprint

Journal article

Revealing the unseen: 3D synchrotron X-ray imaging of uterine vasculature in adenomyosis

VMW Michels, A Szmul, J Jacob, H Dejea, BS de Bakker, JAF Huirne, HOAHub Uterine Consortium

Angiogenesis 29(1), 3 (2026). Paper

Journal article

Multiscale segmentation using hierarchical phase-contrast tomography and deep learning

Y Zhou, S Aslani, Y Javanmardi, J Brunet

PLOS Computational Biology 22(2), e1013923 (2026). Paper

20255 publications
Preprint

Resolving near-micron scale features within a whole sheep head using Hierarchical Phase-Contrast Tomography

T Urban, J Brunet

bioRxiv preprint (2025). Preprint

Book chapter

Hierarchical Phase-Contrast Tomography: Advancing High-Resolution Imaging of Intact Human Organs

J Brunet

In Gray's Anatomy, 43rd edition (2025). Book chapter.

Preprint

Multimodal X-ray imaging reveals hierarchical fibre mechanics

E Newham, AL Parmenter, J Chen, C Disney, T Snow, J Brunet

bioRxiv preprint (2025). Preprint

Journal article

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography

S Rahmani, DJ Jafree, PD Lee, P Tafforeau, J Brunet

npj Imaging 3(1), 39 (2025). Paper

Journal article

Eikonal phase retrieval: Unleashing the fourth generation sources’ potential for enhanced propagation-based tomography on biological samples

A Mirone, J Brunet

Journal of Synchrotron Radiation 32(5) (2025). Paper

20245 publications
Journal article

Deep learning for 3D vascular segmentation in hierarchical phase contrast tomography: a case study on kidney

E Yagis, S Aslani, Y Jain, Y Zhou, S Rahmani, J Brunet

Scientific Reports 14(1), 27258 (2024). Paper

Proceedings

Hierarchical phase-contrast tomography: A non-destructive multiscale imaging approach for whole human organs

J Brunet, CL Walsh, P Tafforeau, H Dejea, AC Cook, A Bellier, K Engel, DD Jonigk, M Ackermann, PD Lee

Developments in X-Ray Tomography XV, 1315216 (2024). Paper

Journal article

Imaging three-dimensional airway morphology in congenital pulmonary airway malformation using hierarchical phase-contrast tomography

SE Verleden, T Urban, J Brunet

American Journal of Respiratory and Critical Care Medicine (2024). Paper

Journal article

Multidimensional analysis of the adult human heart in health and disease using hierarchical phase-contrast tomography (HiP-CT)

J Brunet

Radiology 312(1), e232731 (2024). Paper

Journal article

A closer look at high-energy X-ray-induced bubble formation during soft tissue imaging

RP Xian, J Brunet, Y Huang, WL Wagner, PD Lee, P Tafforeau, CL Walsh

Journal of Synchrotron Radiation 31(3), 566–577 (2024). Paper

20233 publications
Journal article

Preparation of large biological samples for high-resolution, hierarchical, synchrotron phase-contrast tomography with multimodal imaging compatibility

J Brunet

Nature Protocols 18(5), 1441–1461 (2023). Paper

Journal article

Comment on: Intrapulmonary shunt and alveolar dead space in a cohort of patients with acute COVID-19 pneumonitis and early recovery

M Ackermann, P Tafforeau, J Brunet

European Respiratory Journal 61(2) (2023). Paper

Journal article

In situ visualization of aortic dissection propagation in notched rabbit aorta using synchrotron X-ray tomography

J Brunet, B Pierrat, J Adrien, E Maire, BA Lane, N Curt, A Bravin, N Laroche, P Badel

Acta Biomaterialia 155, 449–460 (2023). Paper

20213 publications
Journal article

A parametric study on factors influencing the onset and propagation of aortic dissection using the extended finite element method

J Brunet, B Pierrat, P Badel

IEEE Transactions on Biomedical Engineering 68(10), 2918–2929 (2021). Paper

Journal article

A novel method for in vitro 3D imaging of dissecting pressurized arterial segments using X-ray microtomography

J Brunet, B Pierrat, J Adrien, E Maire, N Curt, P Badel

Experimental Mechanics 61, 147–157 (2021). Paper

Journal article

Review of current advances in the mechanical description and quantification of aortic dissection mechanisms

J Brunet, B Pierrat, P Badel

IEEE Reviews in Biomedical Engineering 14, 240–255 (2021). Paper

20191 publication
Journal article

A combined experimental-numerical lamellar-scale approach of tensile rupture in arterial medial tissue using X-ray tomography

J Brunet, B Pierrat, J Adrien, E Maire, P Badel

Journal of the Mechanical Behavior of Biomedical Materials 95, 116–123 (2019). Paper

Back to top