Thèse Imagerie Multimodale de l'Organisation Tissulaire 3D de l'Instrumentation à l'Imagerie Computationnelle par Apprentissage Non Supervisé H/F - Doctorat.Gouv.Fr

Établissement : Université Claude Bernard Lyon 1
École doctorale : MEGA - Mécanique, Énergétique, Génie Civil, Acoustique
Laboratoire de recherche : CREATIS - Centre de Recherche en Acquisition et Traitement de l'Image pour la Santé
Direction de la thèse : Francois VARRAY ORCID 0000000206665607
Début de la thèse : 2026-10-01
Date limite de candidature : 2026-04-30T23:59:59

Le projet doctoral vise à proposer une imagerie multimodale de l'organisation tissulaire 3D du muscle cardiaque. Pour cela, il sera nécessaire de développer une plateforme d'imagerie tomographique 3D, de proposer des méthodes de reconstruction à l'aide de réseaux implicites et de valider l'approche par comparaison avec d'autres modalités d'imagerie.

The heart is a complex organ that performs the essential function of circulating blood in the human body. This function is crucial to life, and heart disease remains a fundamental cause of death in industrialised countries. The development of diagnostic tools or therapeutic methods requires a detailed understanding of the heart's physiology: the motion/deformation of the muscle, hemodynamics in the various cavities, electrical activation, etc. Moreover, since the heart consists of muscle fibres, it is also relevant to image the local fibrous structure of the tissue as finely as possible to establish a link between this local structure and heart function and, more generally, with the development of various pathologies.

Based on MRI imaging of water diffusion in tissue, CREATIS is one of the leaders in cardiac fibre imaging. This imaging type is very complex, primarily because of the rapid, significant motion of the heart during MRI acquisition. In addition, thanks to the emergence of ultrafast plane-wave ultrasound imaging, the first technique for imaging tissue structure by ultrasound has recently been developed [1]. Ultrasound has many advantages over MRI, including its much lower cost, portability, and, for our application, its high acquisition speed, particularly in ultra-fast imaging.

As part of the laboratory work [2-3], the technique was developed and validated across various experimental environments, including multiplexed US arrays. Based on specific signal-processing developments and new geometric considerations, the US technique appears mature for comparison with other imaging modalities and for evaluating its impact during infarction.

Objectives
To complete this PhD project, several aspects will have to be investigated:
1.Full 3D acquisition and post-processing: Using the Discovery ultrasound system , the 2D US probe can now be fully addressed and controlled, without any restrictions compared to the Vantage system. The standard sequence can now be quickly adapted to acquire any dataset with a given number of transmissions. The post-processing must then be adapted to the existing expertise at Creatis and improved using GPU-based computing to reduce the reconstruction time to a couple of seconds. This pipeline will be validated against nylon-based mono-oriented fantom.
2.3D+anisotropy tomography platform: Using the previous acquisition pipeline, a 3D tomography platform must be designed to acquire a large volume of the heart sample, as illustrated in Fig. 1. The probe rotation must be automatically controlled from the host computer. Each elementary volume will have to be merged, in particular, the local orientation of the heart muscle. The platform validation can first be conducted on standard agar fantom and then on nylon-based media.
3.Methodological development: Once the tomographic data are acquired and merged, two main parameters must be extracted: the volume intensity and the local orientation. Such extraction may be conducted using an implicit neural representation, as it is beginning to be used in medical imaging [4] or in the team [5]. Similar development have also been proposed in photoacoustic imaging [6]. This processing step must be conducted to extract the two main parameters. Moreover, additional considerations, such as changes in attenuation or sound speed, could be considered.
4.Clinical validation: It will be carried out in collaboration with the Creatis MRI team, with which links already exist. Thanks to an established animal protocol, it will be possible to participate in various operations on pigs during open-heart surgery. After the surgery, the heart is removed and imaged using diffusion MRI. Then, the heart can be imaged on the US tomography platform to compare its accuracy and demonstrate the potential of US anisotropy imaging. In addition, the MRI team has expertise in the creation of ischaemia and reperfusion. The value of ultrasound measurement can therefore be assessed in the face of this clinical problem.

Étudiant issu d'une grande école d'ingénieurs (profil généraliste ou EEA), spécialisé dans le traitement de l'image et du signal, l'imagerie par ultrasons, les mathématiques, etc.