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Thesis defense – Tom Delaire

24 November 2022 / 09:30

Venue: Module 2.4 bât CROUS 2ème étage

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Defense in english

Tom Delaire
Theses supervisor: Jean-Baptiste Sibarita


3D high-content screening of spheroids development using soSPIM


Over the last decades, 3D cell cultures have emerged as future gold standards for drug screening and toxicity assays. 3D cell cultures encompass a wide range of samples, ranging from spheroids derived from a single cell line, to organoids derived from stem cells that develop into multicellular organ-like structures, reproducing part of the morphology and functions of human organs. Investigating the development of these 3D cultures is particularly interesting because they faithfully mimic the behaviors observed in vivo, contrary to their 2D counterparts still massively used nowadays. They could also help reducing the number of experiments performed on animals, which is a subject of numerous ethical debates. To achieve this, there is a need to develop dedicated experimental tools, such as high-throughput screening, which is an analysis method based on the automated study of a large number of samples. Their adaptation for 3D cell cultures still poses many challenges, such as: (i) to standardize and parallelize the culture of the 3D samples, while minimizing their manipulation; (ii) to use fast and noninvasive 3D imaging methods to monitor the development of a high number of samples over time, while preserving their biological integrity; (iii) to be compatible with high-content screening protocols to provide sufficient statistics for robust and relevant information extraction; (iv) to integrate dedicated analytical tools for the systematic phenotypic analysis of large data-sets.

To reach these goals, our team, in collaboration with the MechanoBiology Institute in Singapore, have developed the single-objective light-sheet microscopy technology (soSPIM). This imaging method relies on micro-fabricated devices integrating 45° micro-mirrors to create a sheet of light perpendicular to the optical axis of the microscope, and to collect the fluorescence with only one objective. Compatible with any inverted microscope, this architecture removes the mechanical constraints of the standard multi-objectives light-sheet microscopes. New devices called JeWells, composed of truncated pyramidal shaped micro-cavities, have been recently developed. They allow to parallelize and standardize the culture and soSPIM imaging of hundreds of 3D samples within a single chip.

My PhD project aims to develop an innovative platform for 3D high-content screening of 3D cell cultures using the soSPIM technology. I first developed several tools and protocols to automatize the acquisition process and facilitate the handling of the system. In particular, I developed an automatic repositioning software to stabilize and parallelize the 3D screening of samples over days. Second, I implemented several image improvement methods for soSPIM, such as multiview imaging, deconvolution, or optical sectioning by structured illumination, to optimize the quality of the images and improve the performances of the quantification pipeline.

Keywords: Light sheet microscopy, 3D cell cultures, High-Content Screening, 3D live imaging, Deconvolution, Multiview Imaging, Optical sectioning using structured illumination


A. Beghin, G. Grenci, G. Sahni, S. Guo, H. Rajendiran, T. Delaire, S. Binte Mohamad Raffi, D. Blanc, R. de Mets, H.T. Ong, X. Galindo, A. Monet, V. Acharya, V. Racine, F. Levet, R. Galland, J.B. Sibarita, V. Viasnoff, Nature Methods, 2022


  • Jean-Baptiste Sibarita (directeur de thèse) – IINS, Bordeaux, France
  • Virgile Viasnoff (co-directeur de thèse) – MBI, Singapour, Singapour
  • Corinne Lorenzo – Restore-Lab, Toulouse, France (rapporteure)
  • Alexandra Fragola  – ESPCI, Paris, France  (rapporteure)
  • Pierre-François Lenne – IBDM, Marseille, France
  • Gaelle Recher  – LP2N, Talence, France
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24 November 2022
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