Fluctuations microscopy for functional imaging of organoids
Phase contrast microscopy and fluorescence microscopy are the two pillars of modern biological imaging. Phase contrast reveals the morphology of the sample, while fluorescent labeling provides specificity to the process of interest. In both cases, the image is the average value of the measured signal. In this thesis, we propose to focus not on the average value, but on the fluctuations observed in phase contrast. This new contrast will be called Fluctuations Imaging. The fluctuations arise from the active and passive transport phenomena that characterize cellular machinery, and it can be assumed that the level of fluctuations is correlated with cellular activity. The objective of the thesis is to detect phase contrast fluctuations, quantify them, and link them to a process of interest using machine learning methods. The object of study will be lymphocyte activation, which is a critical parameter for monitoring rejection in certain patients with type 1 diabetes who have undergone islet transplantation. Fluctuations Imaging would enable tracking without labeling, simplifying the monitoring protocol. The expected work is (i) optimizing a phase contrast microscope to detect fluctuations, (ii) analyzing image sequences to quantify them, and (iii) implementing the developed method on various biological models, some of which will be pancreas-on-a-chip organs. This thesis, at the intersection of instrumentation, biophysics, and biology, is intended for a student with a background in optics, physics, or equivalent, with a good knowledge of image processing and a strong interest in applications in biology and health.
Development of injectable adhesive hydrogels for the treatment of retinal tears
Retinal tears then detachment, a serious eye condition (20–25 cases per 100,000 in France each year), requires urgent surgery. Current treatments involve removing the vitreous, using gas as a tamponade agent, and sealing tears with laser. However, this method presents drawbacks, including patient restrictions (e.g., prolonged lying down) and complications (e.g., cataracts). Injectable hydrogels are being explored as alternative tamponade agents, but they do not display adhesive properties to suture the tears and laser treatment is still required. Surgical glues have also been tested, but cyanoacrylate-based adhesives are toxic, fibrin-based sealants are hard to use in the eye, and current hyaluronan (HA)-based materials lack sufficient stability and adhesion.
This PhD project aims to develop a sterile, injectable HA-based hydrogel with strong adhesive properties to seal retinal tears. Key requirements include biocompatibility, injectability (30G needle), tissue adhesiveness (1.5–3.7 N), and rapid delivery (within 1 hour). Our group has previously developed an injectable HA hydrogel with dynamic crosslinking, offering long-term stability, biocompatibility, and optical transparency. To confer it with tissue-adhesion properties, two strategies will be tested: (1) addition of tissue-adhesive tannic acid in the hydrogel formulation, or (2) grafting tissue-adhesive groups onto the HA backbone. The hydrogel will be tested for its biocompatibility and adhesiveness in preclinical eye models.
This innovative hydrogel could simplify retinal surgery, reduce complications, lower costs, and improve recovery. Beyond retinal repair, it may have applications in cornea surgery and other medical fields.
Optical intradermal sensing via instrumented microneedles
Cortisol plays a central role in regulating the circadian cycle and in many essential physiological processes such as energy metabolism and immune response. Conventional monitoring of cortisol relies on single blood or saliva samples, which do not accurately reflect the temporal dynamics of its secretion. It is therefore necessary to develop innovative approaches that enable continuous, minimally invasive, and reliable measurement of cortisol concentration in patients.
The doctoral project aims to develop an original optical instrumentation system coupled with microneedles functionalized with fluorescent aptamers for continuous, minimally invasive intradermal monitoring of cortisol without the need for sampling. Within this framework, the PhD candidate will be responsible for designing and sizing the future optical microneedles intended for cortisol detection. They will set up the experimental systems required to characterize the optical microneedles fabricated within the department and test their performance in a representative environment. Finally, the PhD candidate will develop a comprehensive data processing and analysis methodology to identify the key parameters that establish a quantitative relationship between the collected signals and cortisol concentration. Altogether, this work will contribute to the development of an innovative measurement device based on cutting-edge optical emission and detection technologies available at CEA Leti, combining precision, sensitivity, compactness, and thus compatibility with in situ use.
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, 40% of 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 and multiparametric monitoring of a microfluidic chip of the blood-brain barrier model
The blood-brain barrier (BBB) protects the brain by controlling exchanges between the blood and nervous tissue. However, current models struggle to accurately reproduce its complexity. This thesis aims at developing and evaluating a microfluidic chip of BBB model incorporating a real-time monitoring system that combines simultaneous optical and electrical measurements. The device will enable the study of permeability, transendothelial resistance and cellular response to various pharmacological or toxic stimuli. By combining microtechnologies, cell co-cultures and integrated sensors, this model of biological avatar will offer a more physiological and dynamic approach than conventional in vitro systems to improve understanding of the diffusion/permeation phenomena of therapeutic molecules. This project will contribute to the development of predictive tools for neuropharmacology, toxicology and research into neurodegenerative diseases.