Visualising fish oocytes using AI and 3D imaging

Background and challenges

In multiple-spawning fishes, oogenesis involves anatomical structures in permanent renewal, the ovarian follicles, which accompany the development of the gametes until spawning. Despite the identification of numerous regulatory mechanisms of oogenesis in model fish (e.g. medaka, zebrafish), we still have an incomplete and mainly qualitative view of this dynamic process. In particular, major questions remain unanswered: Is there a detectable ageing of ovarian function? What are the key controls on ovarian follicles at different stages of maturity and to what extent is the follicle population self-controlled?

Goals

The IMMO project proposes to exploit new 3D imaging and Artificial Intelligence (AI) methods to visualise and enumerate the completeness of oocytes in fish ovaries at different ages, in order to comprehensively and quantitatively describe the entire population of ovarian follicles and oocytes.

These data will be used to validate a mathematical model describing follicular dynamics and their controls over the life span of the fish, which will reveal information not available from the data alone. The model simulations will reproduce the different types of disturbances affecting the proper functioning of oogenesis.

Contact - coordination 

Partnerships

INRAE participants

Partners

Publications

Journal articles

•  Guillaume Ballif, Frédérique Clément, Romain Yvinec. Nonlinear compartmental modeling to monitor ovarian follicle population dynamics on the whole lifespan. Journal of Mathematical Biology, 2024, 89 (9), pp.43. ⟨10.1007/s00285-024-02108-6⟩. ⟨hal-03739205v2⟩ 
• Guillaume Ballif, Frédérique Clément, Romain Yvinec. Averaging of a stochastic slow-fast model for population dynamics: application to the development of ovarian follicles. SIAM Journal on Applied Mathematics, 2022, 82 (1), pp.359-380. ⟨10.1137/21M1409615⟩. ⟨hal-03405177⟩ 
• Manon Lesage, Manon Thomas, Thierry Pécot, Tu-Ky Ly, Nathalie Hinfray, et al.. An end-to-end pipeline based on open source deep learning tools for reliable analysis of complex 3D images of ovaries. Development (Cambridge, England), 2023, 150 (7), pp.dev201185. ⟨10.1242/dev.201185⟩. ⟨hal-04062159⟩ 
• Frédérique Clément, Louis Fostier , Romain Yvinec. Well-posedness and bifurcation analysis of a size-structured population model: Application to female gametes dynamics. hal-04699357v1 (https://hal.science/hal-04699357)

Conference papers

• Manon Lesage, Jérôme Bugeon, Manon Thomas, Thierry Pécot, Violette Thermes. Mise en application d'algorithmes open-source de Deep-Learning pour l'analyse d'images 3D d'ovaires de Médaka. 11. Journées Scientifiques et Techniques du Réseau des Microscopistes INRAE, Nov 2022, Rennes, France. ⟨hal-04046034⟩
• Manon Lesage, Jérôme Bugeon, Manon Thomas, Stéphanie Gay, Thierry Pécot, et al.. A comprehensive 3D approach to unravel follicular growth dynamics that governs fecundity in medaka fish (Oryzias latipes). 14. International Congress on the Biology of Fish, Jun 2022, Montpellier, France. ⟨hal-03764407⟩ 
• Manon Lesage, Mak Sully, Jérôme Bugeon, Manon Thomas, Stéphanie Gay, et al.. Quantitative analysis of asynchronous oogenesis dynamics in fish: Application of a modern 3D analysis approach to an old problem. 12. International Symposium on Reproductive Physiology of Fish (ISRPF), May 2023, Chersonissos, Greece. ⟨hal-04187726⟩
• “Fish oogenesis modelling”, Louis Fostier, Journées Math Bio Santé 2023 Marne La Vallée, France, “Using Artificial Intelligence to study ovarian development in model fish”, ITMO BCDE, May 2024, Paris, France. https://hal.inrae.fr/hal-04745239. Oral presentation. 
•  ​​​​​​“Fish oogenesis modeling : oocyte population dynamics”, Frédérique Clément , Louis Fostier , Manon Lesage, Violette Thermes, Romain Yvinec, ECMBT (European conference on mathematical and theoretical biology), 2024. Poster presentation (best poster award) 
•   ​​​​​“A model of oocyte population dynamics for fish oogenesis », Louis Fostier, Biology  and Medicine Through Mathematics Conferecence (BAMM), May 2024 Richmond (VA) USA.
•  Time scale separation in life-long ovarian follicles population dynamics model, Romain Yvinec, Biology  and Medicine Through Mathematics Conferecence (BAMM), May 2024 Richmond (VA) USA.