Internship proposal: Development and Optimization of Registration Algorithms for Multimodal In Vivo Imaging

! CLIQUER ICI POUR LA VERSION FRANÇAISE !

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Type of internship

Final-year internship (final year of Master’s degree or engineering school).

Internship date or duration

First semester of 2026, for a duration of 5 to 6 months (flexible dates).

Context

Ultrasound Localization Microscopy (ULM) is an imaging technique that combines high frame-rate (so-called ultrafast) ultrasound with the localization and temporal tracking of injectable contrast agents (microbubbles). This modality yields super-resolved images of the microvasculature, achieving spatial resolution on the order of 20 µm. ULM enables fine characterization of 3D vascular architecture, analysis of its spatial distribution, and quantification of blood flow at a scale previously inaccessible with conventional ultrasound [1][2]. Additionally, further processing of the data can yield lower-resolution maps of perfusion, known as ultrafast Doppler images. However, the performance of ULM can be significantly degraded by motion in the imaged region during acquisition.

The PETRUS system integrates Positron Emission Tomography (PET) with 3D ultrafast Doppler imaging. This multimodal platform allows the overlay of functional maps that describe both metabolism (PET) and blood perfusion (Doppler) [3]. Coupling ULM with the PETRUS system is currently under investigation as part of a PhD project at the LIB, aiming to study vascular and metabolic disruptions in cancerous lesions. Doppler images are acquired using both PETRUS and ULM, which may allow them to be aligned within the same spatial reference frame.

This internship will support ongoing research conducted by two PhD students (Léa Davenet and Jean-Baptiste Deloges) at the LIB, focusing on: (1) the alignment of 3D images acquired with PETRUS and ULM, and (2) the correction of physiological motion (respiration, cardiac activity) as well as operator- and patient induced motion in ULM imaging. For task (1), the intern will work with preclinical data acquired on tumor models using ULM/PETRUS to investigate the relationships between vascular architecture and metabolic activity. For task (2), additional datasets will include clinical ULM acquisitions in stroke patients and preclinical ULM acquisitions of native kidneys. These datasets will be incorporated to enable translational evaluation.

Objective

This project aims to design and implement spatial registration algorithms for 3D images affected by motion or acquired through distinct imaging modalities. The intern will contribute to the development of these tools, validate them on experimental in vivo data (both human and animal), and help integrate them into existing analysis pipelines.

Tasks

  • Conduct a review of the state of the art and existing approaches;
  • Develop tools for aligning images from different modalities;
  • Implement and optimize motion correction algorithms;
  • Evaluate the developed methods on in vivo datasets;
  • Compare the performance of the different approaches;
  • Integrate the solutions into existing processing pipelines.

Required skills

We are looking for a Master’s or engineering student with a background in signal and image processing.

Experience in programming (Python and/or MATLAB), gained through an internship or academic project, is expected.

Knowledge of medical imaging or an interest in medical applications will be appreciated.

References

  1. Christensen-Jeffries, K., Couture, O., Dayton, P. A. et al. Super-resolution Ultrasound Imaging. Ultrasound in Medicine & Biology 46, 4 (2020). https://doi.org/10.1016/j.ultrasmedbio.2019.11.013
  2. Chabouh, G., Denis, L., Abioui-Mourgues, M. et al. 3D transcranial ultrasound localization microscopy in awake mice: protocol and open-source pipeline. Commun Eng 4, 102 (2025). https://doi.org/10.1038/s44172-025-00415-4
  3. Provost, J., Garofalakis, A., Sourdon, J. et al. Simultaneous positron emission tomography and ultrafast ultrasound for hybrid molecular, anatomical and functional imaging. Nat Biomed Eng 2, 85–94 (2018). https://doi.org/10.1038/s41551-018-0188-z

Compensation

Monthly internship stipend (according to current French regulations), and partial reimbursement of monthly public transport costs (≃€550–600/month total).

Contact

Candidates are invited to send their CV, cover letter, and transcripts from the last two academic years to:

  • Léa Davenet (lea.davenet[at]sorbonne-universite.fr)
  • Jean-Baptiste Deloges (jean-baptiste.deloges[at]sorbonne-universite.fr)
  • Jérôme Gâteau, PhD (jerome.gateau[at]sorbonne-universite.fr).

Lieu du stage

This internship will be carried out within the “Medicine and Ultrasound” team at the Laboratory of Biomedical Imaging (LIB), 15 rue de l’École de Médecine, 75006 Paris, France.