Master MVA 2025-2026 First Semester - Medical Image Analysis based on generative, geometric and biophysical models

Hervé Delingette
Equipe Epione
2004, route des Lucioles B.P. 93
06902 Sophia Antipolis Cedex
https://team.inria.fr/epione/en/
04 92 38 77 64
Herve.Delingette@inria.fr

Xavier Pennec
Equipe Epione
2004, route des Lucioles B.P. 93
06902 Sophia Antipolis Cedex
https://team.inria.fr/epione/en/
04 92 38 76 64
xavier.pennec@inria.fr

Course Objectives

The course is an advanced introduction to the mathematical and computing tools used in medical image analysis, ranging from generic image analysis such as image registration and image segmentation to more advanced techniques in statistical and mechanical modeling for computational anatomy and physiology.

Classes are given on Tuesday afternoons from 14:00 to 17:15 at ENS Saclay in room 1Z25 (bât Nord, 1er étage)

The examination consists in the group study of a research article with a report and a 10 min presentation and a multiple choice questionnaire

Liste of courses, slides, course notes and additional material (updated in real-time)

• Tuesday Sept 30, 2025, 14:00-17:15 (ENS Saclay, salle 1Z25) Introduction to Medical Image Acquisition, Image Registration [Xavier Pennec]
  • Slides on image registration
  • Video du cours de 2020 (in French)
• Tuesday Oct 7, 2025, 14:00-17:15 (ENS Saclay salle 1Z25) Image Filtering and Segmentation [Hervé Delingette]
  • Slides on image filtering
  • GitLab for all notebooks
• Tuesday Oct 14, 2025, 14:00-17:15 (ENS Saclay, salle 1Z25) Riemanian Geometry and Statistics [Xavier Pennec]
  • Slides.
  • Video of the course
  • Course notes: Introduction to differential and Riemannian Geometry
  • Course notes: The example of rotations
  • Course notes: Intrinsic Statistics on Riemannian Manifolds: Basic Tools for Geometric Measurements [Another presentation by Tom Fletcher: Statistics on manifolds]
• Tuesday Oct 21, 2025: 14:00-17:15 (ENS Saclay, salle 1Z25) Image Segmentation based on Clustering [Hervé Delingette]
  • Slides
  • The video of the 2023 course (in English)
  • Notebook for K-means for Brain Segmentation
  • GitLab for all notebooks
• Tuesday Oct. 28, 2025: 14:00-17:15 (ENS Saclay, salle 1Z25) Clustering and Markov Random Fields for image segmentation [Hervé Delingette]
  • Slides
  • Lecture Notes on ELBO, EM and Gaussian Mixtures
  • Notebook for Gaussian Mixture Models for Brain Segmentation
  • Notebook for K-means for Brain Segmentation
  • Notebook for Gaussian Mixture Models for Brain Segmentation with bias field correction
  • Course video
  • GrabCut Segmentation
  • Random Walker Segmentation
• Tuesday Nov 4, 2024: 14:00-17:15 (ENS Saclay, salle 1Z25) Analysis in the space of Covariance Matrices [Xavier Pennec]
• Slides
• Video du cours de 2020 (in French)
• Course notes: Manifold valued image processing with SPD matrices
• Tuesday Nov 18 2025: 14:00-17:15 (ENS Saclay, salle 1Z25) Diffeomorphic Registration and Computational Anatomy [Xavier Pennec]
  • Slides
  • Course notes: Beyond Riemannian Geometry: The affine connection setting for transformation groups
• Tuesday Nov 25 2025: 14:00-17:15 (ENS Saclay, salle 1Z25) Active Deformable Models and Shape constraints for image segmentation [Hervé Delingette]
  • Slides
  • Course video
• Tuesday Dec 2, 2025, 13:00-17:15 (Visio) Exam [Hervé Delingette, Xavier Pennec].

Resources

• Online lectures and courses at College de France

Examination Session

• 13h00 G1 Maxime Muhlethaler, Titouan Pottier, Nicolas Beaujoin : Local contrastive loss with pseudo-label based self-training for semi-supervised medical image segmentation. (Chaitanya et al).
• 13h20 G2 Zhenjia Xu, Daniel Kuznetsov : "Synomaly noise and multi-stage diffusion: A novel approach for unsupervised anomaly detection in medical images" (Bi et al).
• 13h40 G3 Enzo Azzoug, Martin De Bats : "Anatomically plausible segmentations: Explicitly preserving topology through prior deformations" (Wyburd et al).
• 14h00 G4 Aina Tiffney, Hugo Naranjo : "Myocardial strain computed at multiple spatial scales from tagged magnetic resonance imaging: Estimating cardiac biomarkers for CRT patients" (Sinclair et al).
• 14h20 G5 Mathilde Morhain, Imane Haddouchi, Karina Musina: "PatchCL-AE: Anomaly detection for medical images using patch-wise contrastive learning-based auto-encoder"
• 14h40 G6 Yannaël Bossard, Deodato Vasconcelos Bastos Neto: "ImUnity: A generalizable VAE-GAN solution for multicenter MR image harmonization" (Cackowski et al., 2023)
• 15h00 G7 Lucien Delpla, Tom Pitois et Maxence Adly: "A geometric approach to robust medical image segmentation" (Santhirasekaram et al.)
• 15h20 G8 Alejandro Argüelles Trujillo et Álvaro Ruiz Lopez: "Multimodal representations of biomedical knowledge from limited training whole slide images and reports using deep learning"
• 15h40 G9 Khoutaibi Iliass, Khalil Yacine and Baraka Rayane: "Quantifying Extrinsic Curvature in Neural Manifolds" (Acosta et al.)
• 16h00 G10 Hamza Azzouzi, Oussama Zouhry: "Factorizer: A scalable interpretable approach to context modeling for medical image segmentation" (Ashtari et al.)
• 16h20 G11 Octave Leroy, Jean-François Guerrero et Lahna Bekri: "Label refinement network from synthetic error augmentation for medical image segmentation"
• 16h40 G12 Alexandre Noel, Octave Jeanne et Aicha Kenani : "Rigid Motion Invariant Statistical Shape Modeling based on Discrete Fundamental Forms (Ambellana et al.)"
• 17h00 G13 Amine Ould Hocine, Valentin Phou et Samuel Povoa: "NePhi: Neural Deformation Fields for Approximately Medical Image Registration"
• 17h20-17h40 Quizz"