Shape analysis

Mailing list and seminar

This website is home to the French research community on shapes analysis, from biomedical imaging to computer assisted design and graphics.

We organize an open seminar in Paris and diffuse announcements related to relevant software tools, conferences and job offers. You may subscribe to the mailing list, feel free to invite newcomers in the field (interns, students, engineers…).

Shape seminar

Every three weeks, we organize an in-person seminar in Paris around noon:

  • 60mn of informal discussions, followed by a 60mn presentation.
  • you are welcome to share the free lunch we provide.
  • Videos for most presentations are available on YouTube (click here).


Wednesday, 12 or 19 June 2024 — How to build a realistic model of the heart?

Time: 12pm
Location: Jussieu - room TBA.
Speaker: Philippe Moireau (Inria Saclay, MediSim team)
Abstract: Philippe will present his work the simulation of biomechanical systems such as the ones encountered in cardiac mechanics, taking into account non-linear mechanics, active soft tissues, fluid-structure interactions, poroelasticity and reaction-diffusion.

Wednesday, 15 May 2024 — A Lagrangian method for fluids with free boundaries

Time: 12pm
Location: Jussieu - room TBA.
Speaker: Bruno Lévy (Inria Saclay, ParMA team)
Abstract: In this presentation, I’ll describe a numerical simulation method for free-surface fluids. I will start by giving an intuitive understanding of the physical phenomena involved in fluid dynamics, pressure, viscosity and surface tension. Then I will detail the numerical simulation method, based on the Gallouet-Mérigot numerical scheme, that describes the fluid as a set of cells, that can deform, but that keep a constant volume, and that follow the motion of the fluid (Lagrangian method). The constant volume constraint takes the form of a partial semi-discrete optimal transport. I will present the geometric and numerical aspects of this optimal transport problem.

Wednesday, 10 April 2024 — Shape optimization problems on discrete surfaces

Time: 12pm
Location: Jussieu - room 15-16.309: between towers 15 and 16, on the 3rd floor.
Speaker: Josua Sassen (École Normale Supérieure Paris-Saclay)
Abstract: Josua will present his work on surface segmentation and design with applications to architecture, mechanical engineering and graphics.

Wednesday, 20 March 2024 — Non-rigid shape matching with intrinsic methods

Time: 12pm
Location: Jussieu - room 15-16.105 for lunch at noon, 15-16.413 for the talk at 1pm.
Speaker: Robin Magnet (GeoVic team, LIX, Ecole Polytechnique)
Abstract: Robin will present his work on functional maps, including his pyFM library.
Links: video

Wednesday, 28 February 2024 — scikit-shapes, a transparent package for statistical shape analysis

Time: 12pm
Location: Seminar room of the MAP5 laboratory, 45 rue des Saints-Pères in Paris (7th floor) - detailed path.
Speaker: Louis Pujol (Université Paris-Cité, HeKA team)
Abstract: Louis will present the first (beta) release of the scikit-shapes library. The talk will be followed by an informal lab session - feel free to bring your laptop! Links: tutorial, GitHub, documentation, one-page gallery.
Links: video slides

Wednesday, 7 February 2024 — From cryo electron microscopy data to continuous conformational landscapes of biomolecules

Time: 12pm
Location: Jussieu - room 15-16.309: between towers 15 and 16, on the 3rd floor.
Speaker: Slavica Jonic (IMPMC – UMR 7590 CNRS, Sorbonne University)
Abstract: The elucidation of different conformations of biomolecular complexes is the key for understanding the molecular mechanisms behind the biological functions of the complexes and the key to novel drug discovery. Single particle analysis (SPA) is a data collection and analysis technique of cryo electron microscopy (cryo-EM) that allows 3D reconstruction of multiple conformations of purified biomolecular complexes from their 2D images. Another cryo-EM technique is cryo electron tomography (cryo-ET), which allows obtaining multiple conformations of the complexes in their cellular environment. Currently, one of the most important and challenging open problems in the cryo-EM field is how to obtain the entire, continuous conformational landscapes of the biomolecules from the data. Consequently, since a few years, methods development to solve this problem has been a very active research area. My group is developing such methods, by combining image processing, molecular dynamics simulations, and deep learning approaches. These methods are made available publicly via our open-source, ContinuousFlex software package, which can be run as a plugin of the broadly used Scipion software package. In this talk, I will present some of our most important achievements regarding this work.
Links: video

Wednesday, 17 January 2024 — Multiscale optimisation for shape registration

Time: 12pm
Location: Jussieu - room 15-25.328: between towers 15 and 25, on the 3rd floor.
Speaker: Fleur Gaudfernau (Université de Paris, HeKA team)
Abstract: Fleur will present her PhD thesis work, done under the supervision of Stéphanie Allassonnière and Erwan Le Pennec.
Links: video

Wednesday, 20 December 2023 — Intrinsic methods for manifold-valued data

Time: 12pm
Location: Jussieu - room 15-16.309: between towers 15 and 16, on the 3rd floor.
Speaker: Elodie Maignant (Inria Sophia and École Normale Supérieure Paris-Saclay)
Abstract: Elodie will present her PhD thesis work, done under the supervision of Xavier Pennec and Alain Trouvé.
Links: video

Wednesday, 6 december 2023 - SMAI-SIGMA day — Constrained diffeomorphometry in computational anatomy.

Time: 10am
Location: Jussieu - room 15-16.309: between towers 15 and 16, on the 3rd floor.
Speaker: Barbara Gris (CNRS, Laboratoire Jacques-Louis Lions)
Abstract: Barbara will present an optimal control framework to perform statistical shape analysis with plausible biological priors.
Links: video

Wednesday, 6 december 2023 - SMAI-SIGMA day — Optimal transport with 3D shapes.

Time: 9am
Location: Jussieu - room 15-16.309: between towers 15 and 16, on the 3rd floor.
Speaker: Jean Feydy (Inria Paris, HeKA team)
Abstract: Jean will present modern optimal transport algorithms, articulating the difference between simple, solved problems in dimension 2 or 3 and NP-hard problems in high dimension.
Links: video slides

Wednesday, 29 November 2023 — Some numerical methods for computer graphics and geometric design

Time: 12.30pm
Location: Jussieu - room 15-25.328: between towers 15 and 25, on the 3rd floor.
Speaker: Josua Sassen (École Normale Supérieure Paris-Saclay)
Abstract: Josua is starting a PostDoc in Paris and will introduce himself with a collection of results from his work in Bonn.
Links: video

Wednesday, 8 November 2023 — The geometry of optimal transport (and Gromov-Wasserstein)

Time: 12pm
Location: Seminar room of the MAP5 laboratory, 45 rue des Saints-Pères in Paris (7th floor) - detailed path.
Speaker: Théo Dumont (Université Gustave Eiffel)
Abstract: Théo will present new results on the structure of the Wasserstein and Gromov-Wasserstein metrics.
Links: video

Wednesday, 11 October 2023 — Open discussion on multiscale methods

Time: 12pm
Location: PariSanté Campus, 10 Rue d’Oradour-sur-Glane. Métro Balard or Porte de Versailles. Seminar room of the HeKA team (3rd floor, South corridor).
Speaker: Louis Pujol and others (Université Paris-Cité)
Abstract: We will have an open chat on multiscale implementations of shape analysis methods, from both practical and theoretical perspectives. You may prepare up to 5 slides to present a method or implementation that you would like to discuss.

Friday, 15 September 2023 — The geometry and topology of shape patterns, with applications to leukaemia

Time: 12pm
Location: Jussieu, room 15-16.309 (i.e. in the corridor that links column 15 to column 16, on the third floor). This is the seminar room of the Laboratoire Jacques-Louis Lions.
Speaker: Anna Song (Imperial College London and The Francis Crick Institute)
Abstract: Anna will present the results of 4 years of work on 3D shape textures. This includes a new generative model based on curvature minimization, contributions to topological data analysis in 3D and a study of the microscopic structure of bone marrow vessels.
Links: video slides

Monday, 26 June 2023, 1/4 — Some open mathematical problems

Time: 12.30pm
Location: Inria Paris centre, 2 rue Simone Iff, A building, ground floor, Emmy Noether room (Startup Studio entrance).
Speaker: François-Xavier Vialard (Université Gustave Eiffel)
Abstract: François-Xavier will present a collection of open mathematical questions related to diffeomorphic registration and residual networks.
Links: slides

2/4 — Modeling structural biology with geometric deep learning

Speaker: Vincent Mallet (École Polytechnique, CNRS)
Abstract: Vincent will present his work on the representation of RNA strands as 2.5D graphs, proteins as surfaces and antibody detection on Cryo-EM images.
Links: video slides

3/4 — Metamorphoses of manifold-valued images

Speaker: Guillaume Sérieys (Université Paris-Cité, MAP5)
Abstract: Guillaume will present his work on the generalization of continuous metamorphoses to images with values in spaces of probability distributions or diffusion tensors.
Links: slides

4/4 — An extended orbit model

Speaker: Thomas Pierron (ENS, Centre Borelli)
Abstract: Thomas will present his work on a hierarchical, multi-scale model for diffeomorphic shape registration.
Links: video slides

Friday, 2 June 2023 — Two Python libraries for 3D visualization

Time: 12.30pm
Location: Seminar room of the MAP5 laboratory, 45 rue des Saints-Pères in Paris (7th floor) - detailed path.
Speaker: Louis Pujol (Université Paris-Cité)
Abstract: Louis will present two modern libraries for visualizing and interacting with 3D shapes, Pyvista and Vedo. The talk will be followed by an informal lab session - feel free to bring your laptop!
Links: video code


Mailing list

To register to shapes@inria.fr, please:

  1. Send a message with title “subscribe shapes Your Name” to sympa_inria@inria.fr.
  2. You will then receive an invite link. Don’t forget to click on it, or you won’t be registered as a subscriber!


Organizers

Sponsors