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Study and implementation of an original optical approach combining diffuse polarization spectrometry and Mueller's method for plant monitoring with the identification of specific phenotypic traits: application to vine water stress

After graduating with a Master 2 in signal and image processing from École Centrale Marseille, I was able to work on a number of research projects in the fields of image processing and artificial intelligence. These different experiences have encouraged me to pursue a career in research.
The aim of this thesis is to apply the latest advances in terms of research in instrumental optics and polarization spectrometry (biospeckle) to the measurement, monitoring and evaluation of plants, in order to better understand their responses to changing crop conditions, particularly in the face of water stress. Sensitive to issues linked to the field of ecology applied to new technologies, these open up a wide spectrum of possibilities, particularly in the new field of intelligent agriculture.

• Starting date: 1st October 2021
• University: Institut Agro 
• PhD school: GAIA
• Scientific field: Agro-resources, Processes, Foods, Bioproducts
• Thesis management: Ryad Bendoula, UMR Itap, Inrae – Thierry Simonneau, Lepse, Inrae
• Thesis supervisors: Arnaud Ducanchez, UMR Itap, Inrae
• Funding: #DigitAg – Institut Agro 
• #DigitAg : Cofunded thesis – Axe 3 : Capteurs, acquisition et gestion de données, Axe 5 : Fouille de données, analyse de données, extraction de connaissances, Challenge 2 : Le phénotypage rapide

Keywords : phenotyping, spectrometry, polarization, Mueller matrix, vine, water stress

Abstract: In a fast-changing global environment, the ability to produce plant material adapted to diverse, changing and sometimes extreme agronomic conditions is an absolute priority. In particular, agriculture must consider possible ways of adapting and managing water resources to maintain sustainable agricultural production. To do this, one of the levers identified is the creation of new varieties that are more tolerant to abiotic stresses. While genotyping capacities have exploded in recent years, identifying the mechanisms involved through phenotyping remains very complex. Thus, the ability to produce relevant phenotyping information remains the limiting factor for the progress of varietal selection. However, instrumental optics, and in particular measurement systems based on visible and near-infrared spectrometry, have demonstrated in recent years that they offer undeniable potential for addressing these demands. But while some gene expression parameters are now accessible, there are other, crucial parameters that are not yet directly measurable. In particular, the measurement of some characteristics of the plant's response to water stress. The aim of this thesis will be to study, implement and evaluate a new and original optical approach that combines polarized light spectroscopy and the Mueller matrix. This technique, which is precise and more targeted, will make it possible to better decrypt the spectra in order to extract and select the main traits and indicators that characterize the varieties and their resistance to hydric stress. This method will be tested on different varieties of grape varieties subjected to different types of hydric stress with measurements taken at the leaf level to avoid the first level of spectral disturbance linked to the plant cover.