Internship proposal: Implementation of advanced super-resolution methods applied to 3D clinical data

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! CLIQUER ICI POUR LA VERSION FRANÇAISE !

 

Download the internship proposal

Internship type

MSc 2nd year or last year of engineering school

Duration

February/March for 6 months

Context

Within the LIB (Laboratory of Biomedical Imaging), you will work in the Physiology and Pathology of Microcirculation (PPM) team, led by Olivier Couture.

Ultrasound Localization Microscopy (ULM) is a super-resolution ultrasound technique based on tracking microbubbles as they flow through blood vessels. These microbubbles are commonly used clinically as ultrasound contrast agents. A tenfold increase in resolution beyond the physical limit has been achieved in vivo in a preclinical rat brain model [Errico et al., 2015]. Since then, ULM has evolved from 2D to 3D imaging [Heiles, 2019], allowing for complete imaging of the target organ. For example, it has become possible to image the entire kidney in small animal models.

Recent advances in animal studies have enabled the launch of a clinical trial to image the brains of stroke patients. With 3D acquisitions, the team has acquired large patient data volumes. These data are challenging to process due to the human skull, which makes signal extraction significantly more difficult. Several signal and image processing methods have recently been proposed in the literature to enhance the contrast of microvessels.

 

A 3D renderings of the rat brain vascularization with the a MRI surface [Chavignon, 2023]

Objective

The objective of this internship is to implement these new methods and test them on a variety of clinical datasets to evaluate their effectiveness compared to our current approach.

Missions

The intern will have the following tasks:

  • Understanding the acquisition and post-processing steps required to achieve 3D ULM.
  • Gaining knowledge of the new post-processing methods.
  • Implementing these new methods.
  • Comparing this implementation with the current method used in the laboratory.

Expected competences

  • Knowledge and practical experience in ultrasound and signal processing.
  • Background in biomedical engineering theory and practice.
  • Proficiency in English for writing and communication.
  • Willingness to work in various research environments (medical imaging laboratory) and interdisciplinary fields (acoustics, biomedical, in vivo studies).
  • Programming skills in Matlab/Python would be a plus.

References

  1. Errico, Claudia, Juliette Pierre, Sophie Pezet, Yann Desailly, Zsolt Lenkei, Olivier Couture, et Mickael Tanter. « Ultrafast Ultrasound Localization Microscopy for Deep Super-Resolution Vascular Imaging ». Nature 527, nᵒ 7579 (novembre 2015): 499‑502. https://doi.org/10.1038/nature16066.
  2. Heiles, Baptiste, Mafalda Correia, Vincent Hingot, Mathieu Pernot, Jean Provost, Mickael Tanter, et Olivier Couture. « Ultrafast 3D Ultrasound Localization Microscopy Using a 32 × 32 Matrix Array ». IEEE TRANSACTIONS ON MEDICAL IMAGING 38, nᵒ 9 (2019).
  3. Chavignon, Arthur, et al. « Deep and Complex Vascular Anatomy in the Rat Brain Described With Ultrasound Localization Microscopy in 3D. » IEEE Open Journal of Ultrasonics, Ferroelectrics, and Frequency Control 3 (2023): 203-209.
  4. Christensen-Jeffries, Kirsten, Olivier Couture, Paul A. Dayton, Yonina C. Eldar, Kullervo Hynynen, Fabian Kiessling, Meaghan O’Reilly, et al. « Super-Resolution Ultrasound Imaging ». Ultrasound in Medicine & Biology 46, no 4 (avril 2020): 865‑91. https://doi.org/10.1016/j.ultrasmedbio.2019.11.013.
  5. L. Denis, G. Chabouh, B. Heiles and O. Couture, « Volumetric Ultrasound Localization Microscopy, » in IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control, https://doi.org/10.1109/TUFFC.2024.3485556

Remuneration

Internship gratification

Contact

Olivier Couture – olivier.couture[at]sorbonne-universite.fr
Jean-Baptiste Deloges – jean-baptiste.deloges[at]sorbonne-universite.fr