Sperm 3D - Male infertility diagnostic tool using holography for imaging and 3D tracking

Infertility is a growing problem in all developed countries. The standard methods for the diagnostic of male infertility examine the concentration, motility and morphological anomalies of individual sperm cells. However, one in five male infertility cases remain unexplained with the standard diagnostic tools.

In this thesis, we will explore the possibility to determine the male infertility causes from the detailed analysis of 3D trajectories and morphology of sperms swimming freely in the environment mimicking the conditions in the female reproductive tract. For this challenging task, we will develop a dedicated microscope based on holography for fast imaging and tracking of individual sperm cells. Along with classical numerical methods, we will use up-to date artificial intelligence algorithms for improving the imaging quality as well as for analysis of multi-dimensional data.

Throughout the project we will closely collaborate with medical research institute (CHU/IAB) specialized in Assisted Reproductive Technologies (ART). We will be examining real patient samples in order to develop a new tool for male infertility diagnosis.

Development of a Multilayer Encapsulation System for the Production of Core-Shell Microcapsules Suitable for Organoid Growth

Every year, 20 million people worldwide are diagnosed with cancer, with 9.7 million succumbing to the disease (Kocarnik et al., 2021). Personalized treatment could significantly reduce the number of deaths. This thesis addresses this challenge by proposing the development of organoids derived from patient biopsies to optimize treatments.

The bioproduction of encapsulated cells in biopolymers is a rapidly growing field, with applications in personalized medicine, research, drug screening, cell therapies, and bioengineering. This thesis aims to contribute to these fields by focusing on the multilayer encapsulation of cells in biopolymers with a wide range of viscosities.

The inner layer (core) provides an optimal environment for the maturation and survival of cells or organoids, while the outer layer (shell) ensures mechanical protection and acts as a filtering barrier against pathogens.

This new thesis aims to design, develop, and study—both analytically and numerically—the architecture of a dual-compartment nozzle for the high-frequency production of monodisperse core-shell capsules. It builds upon a previous thesis completed in 2023, which focused on the detailed characterization and development of a predictive model for the generation of single-layer microcapsules using centrifugal force alone.

The formation and ejection mechanisms of multilayer capsules are complex, involving the rheological properties of biopolymers, centrifugal force, surface tension, and interfacial dynamics. The nozzle architecture must account for these properties.

The first part of this thesis will focus on understanding the multilayer formation and ejection mechanisms of microcapsules as a function of nozzle geometry. This will allow the prediction and control of capsule formation based on the rheological properties of the biopolymers. The second part will involve developing an automated system for the aseptic production of capsules. Finally, biological validation will assess the functionality and reliability of the developed technology.

To achieve the objectives of this study, the candidate will first conduct analytical and numerical studies, design the ejection nozzles, and leverage the laboratory's expertise for their fabrication. Fluidic tests on prototypes will help optimize the design, leading to the development and testing of a fully operational microcapsule production system.

The ideal candidate will have a background in physics, engineering, and fluid mechanics, with a strong inclination for experimental approaches. Prior experience in microfluidics or biology would be a valuable asset.

Ultra-wide-field smart microscope for the detection of egg parasite (SCREENER)

In most parasitic cycles, the free phase passes through an egg stage, which is released by the host into the environment via a complex faecal matrix, which has highly variable and often low egg concentrations. The classical detection method relies on microscopic observation of these eggs, which implies a tedious and time-consuming preparation of the sample to concentrate the eggs, with highly variable sensitivity values. This detection is crucial because, once dispersed, the eggs contaminate the environment and food, leading to cases of parasitic zoonoses in humans.
Detection in environmental and food matrices is even more complex than for faeces because of the very low number of eggs present : 1 to 10 per sample in the vast majority of cases. The thesis aims at developing a lensless wide-field imaging system that will allow the counting and identification of parasite eggs in complex matrices, while increasing sensitivity. This will make it possible to automate detection, thus opening up the possibility of investigating more samples for better health surveillance.

Characterization of motor recovery in stroke patients during a BCI-guided rehabilitation

This thesis will explore the use of implanted brain-computer interfaces (BCIs) for motor rehabilitation in stroke patients. The project leverages Clinatec's WIMAGINE technology, which measures brain activity through electrocorticography (ECoG) to accurately decode patients' motor intentions. Integrating this technology into a rehabilitation protocol is expected to enhance residual motor abilities through neural plasticity. In this context, the thesis aims to implement the rehabilitation protocol with Clinatec's technical and clinical teams and to characterize motor recovery in patients during training sessions, both behaviorally and neurally. The study will include a review of current BCI-assisted rehabilitation approaches, the development of tools to monitor motor progress and measure neural plasticity indicators, as well as the optimization of rehabilitation sessions based on patients' motor performance. Motor and neural progression will be studied longitudinally over nine months, with an extended two-year follow-up to assess the durability of the benefits. Supported by the French Ministry of Research and the EU, this project offers a unique opportunity to establish the foundations of a new post-stroke rehabilitation paradigm using implanted BCIs.

On-line monitoring of bioproduction processes using 3D holographic imaging

The culture of adherent cells on microcarriers (MCs) is a promising approach for various bioproduction applications, such as drug manufacturing and delivery, regenerative medicine, and tracking of cellular differentiation. However, the analysis of single cell morphology and behavior without affecting the substrate integrity remains a major challenge. Lens-free holographic imaging is emerging as a promising solution for real-time, non-invasive monitoring of cellular processes. This technique captures wide field of view images without requiring exogenous labeling or sample manipulation, thus preserving the integrity of the cellular environment.
This thesis proposes the development of a 3D lens-free imaging system to monitor cells on MCs in near real-time. The microscope will be coupled with advanced algorithms for data reconstruction and analysis in on-line bioreactors. The use of deep learning techniques will allow for real-time segmentation and analysis of single cells, facilitating the tracking of cellular dynamics. This innovative project paves the way to a non-invasive monitoring of 3D multicellular samples, with potential applications on organ-on-chip and more complex organoids systems.

New rapid diagnostic tool for sepsis: microfluidic biochip for multi-target detection by isothermal amplification

Sepsis is among the main cause of death across the world, and is caused by severe bacterial infection but can also originate from viruses, fungi or even parasites. In order to drastically increase survival rates, a rapid diagnostic and appropriate treatment is of paramount importance. The commercially available tools for nucleic acid detection by qPCR are able to sense multiple targets. However, these multiplexed analyses arise from the accumulation of analysis channels or reaction chambers where only one target can be detected. The original sample has to be divided, resulting in a loss of sensibility since a smaller amount of targets is available in channels or chambers.
In order to tackle the question of “How to detect multiple targets without a loss in sensibility?”, the PhD candidate will have to develop a multiplexed detection in a single reaction chamber by localized immobilization of LAMP primers (Loop-mediated isothermal amplification) on a solid substrate like COC or glass.
The expected outcome is a biochip allowing for real-time and fast (minutes) detection of several molecular DNA targets including: primers design and selection, primers immobilization on surface, integration of the biochip into a microfluidic cartridge and data collection and management for fluorescence detection of targets.
This innovative work will provide the PhD candidate with strong skills in diverse scientific domains such as molecular biology, surface functionalization, modelling and simulation, in a very multidisciplinary working environment.

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