Thesis offer: Organoid live imaging analysis with AI
Context
As part of the DIM C-BRAINS international PhD program, Kate GRIEVE is looking for a PhD student for her project ORGAI: Analysis of live imaging of organoids using AI.
The ORGAI project brings together two Vision Institute teams expert in imaging and organoid development, and aims to develop AI and machine learning tools to quantify cell specific data. We aim to validate our novel live imaging approach named DFFOCT for label-free, longitudinal imaging of patient-derived organoid models. Our goal is to demonstrate that DFFOCT, combined with AI-driven analysis, can create relevant numerical twins of organoids to predict which drugs will be most effective for individual patients. The PhD student will develop new machine learning and AI models, enabling automatic high-throughput data analysis. These techniques will make it possible to quantify the morphology and viability of each of the organoid's cells, identify their cell types, and monitor their fate. These digital tools will increase the specificity of label-free microscopes, predict biological results from a minimum number of experimental data, and generalize results.
Full thesis project: DIM C-BRAINS
The research team
Kate Grieve’s team, "Live imaging in patients and cells", develops novel imaging technology to discover the health of cells in the patient’s living retina or in the lab.
Missions
The student will learn to use the DFFOCT microscope to image retinal organoids and build the image database for analysis. In parallel, the student will be responsible for the development of the AI and machine learning tools for analysis of the data. The student will interact with the multidisciplinary project team to feedback on results and interpretation. We would like to recruit a student with a primary experience in computer science, programming, and image processing. Secondary experience and/or interest in optics, microscopy and biology would be appreciated.
The PhD project will include the following steps, with some being in parallel:
1. Use of the DFFOCT microscope (M1-M12)
2. Handling retinal organoids and obtaining good images of them (M1-M12)
3. Managing image database (M1-M30)
4. (Main focus): development of AI and machine learning tools (M6-M24)
5. Data analysis using developed tools and feedback to the project team (M12-M30)
6. Dissemination of results (M25-M36)
Skills required
Computer skills, programming and image processing required.
Education and experience
Experience and/or interest in optics, microscopy and biology would be appreciated.
This thesis is funded by the “DIM C-BRAINS” network of the Ile-de-France region.
Funding requires candidates to have completed their Master's training and internship outside France. 60e383d7-92eb-47fa-b76e-e48dd975cc19.pdf
Applications must be submitted ONLY on the DIM C-BRAINS website https://dim-cbrains.fr/en/phd-program/dim-cbrains .
Application deadline: January 31, 2025, for a PhD starting in autumn 2025. Interested candidates can send their questions to kate.grieve@inserm.fr .
Specific working conditions
Doctoral contract - 3 years
How to apply
To apply for this vacancy, please complete this form and attach your cover letter and curriculum vitae in .pdf format. We will get back to you as soon as possible.