Welcome!

I am heading the joint Inria/ICM Aramis Lab with O. Colliot at the Brain and Spine Institute (ICM) located within the Pitié-Salpêtrière hospital in Paris. I am also the coordinator of the ICM Center of Neuroinformatics, and scientific director of the ICM platform of biostatistics and bioinformatics.

My team focuses on the development of new statistical and computational approaches for the analysis of image data and image-derived geometric data such a surface meshes. We have contributed to the definition of statistical analysis methods for spatiotemporal measurements in longitudinal studies, where sets of geometric objects (or structured data) are observed at multiple points in time.

Our research is essentially motivated by, and applied to the study of the structure and function of the human brain. It makes accessible the wealth and complexity of information contained in multiple modalities of medical images via virtual representations of the brain, and allows the tracking of these representations during ageing or disease progression.

I received the Young Investigator Award from the conference MICCAI in 2008 and the second Gilles Kahn Award for best dissertation in computer science in 2010. In 2015, I was awarded an ERC Starting Grant from the European Research Council.

I am associate editor of IEEE Transactions on Medical Imaging.

Breaking News

Latest news...

  • Nov 1:Congratulations to Barbara Gris who has her paper "A sub-Riemannian modular framework for diffeomorphism based analysis of shape ensembles" accepted in SIAM Journal on Imaging Sciences!!
  • Oct 13:Congratulations to Amelie Beaudet who has her paper "The endocranial shape of Australopithecus africanus: surface analysis of the endocasts of Sts 5 and Sts 60" accepted in Journal of Anatomy!!
  • Oct 7:Happy to be on scene for the next edition of S3 Odeon!
  • Sep 29:Congratulations to Jean-Baptiste Schiratti who has his paper "A Bayesian mixed-effects model to learn trajectories of changes from repeated manifold-valued observations" accepted in Journal of Machine Learning Research!
  • Sep 9:Congratulations to Anne Bertrand, who has her paper "Early cognitive, structural and microstructural changes in c9orf72 presymptomatic carriers before 40 years of age" accepted in JAMA Neurology!
  • Jul 12:Congratulations to Manon Ansart who will have an oral presentation at the next conference on Clinical Trials in Alzheimer's Disease (CTAD) in Boston in November, with in addition a paper accepted at Machine Learning in Clinical Decision Systems on "Prediction of amyloidosis from neuropsychological and MRI data for cost effective inclusion of pre-symptomatic subjects in clinical trials"! Big success Manon!
  • Jul 11:Congratulations to Alexandre Bone and Maxime Louis for their paper entitled "Prediction of the progression of subcortical brain structures in Alzheimer’s disease from baseline" which has been accepted at Mathematical Foundations of Computational Anatomy!
  • Jul 3:Congratulations to Maxime Louis and Alexandre Bone for their paper entitled "Parallel transport in shape analysis : a scalable numerical scheme for Riemannian manifolds" which has been accepted at Geometrical Science of Information (GSI)!
  • Jun 30:Our paper entitled "A Bayesian mixed-effects model to learn trajectories of changes from repeated manifold-valued observations" has been accepted for publication in Journal of Machine Learning Research. Congratulation Jean-Baptiste!
  • Jun 29:A portrait has been published in the weekly magazine Reforme
  • May 22:My interview for FrenchWeb.fr has been published here!
  • May 16:Congratulations to Igor Koval who has his paper accepted to MICCAI 2017. The paper is entitled: Statistical learning of spatiotemporal patterns from longitudinal manifold-valued networks
  • Apr 6: Congratulations to Jean Dumoncel, who successfully defended his PhD today at the University of Toulouse!
  • Apr 3:Pan European Networks has published my report on Digital Models of Brain Ageing. Read it here.
  • Mar 20: Our paper "Amyloidosis and neurodegeneration result in distinct structural connectivity patterns in mild cognitive impairment" from Jacquemont et al. has been accepted for publication in Neurobiology of Aging
  • Mar 15: I am happy that French radio "France Culture" has mentioned my work this morning (listen here at 1 minute) with an article in the website of the companion radio "France Inter" there.
  • Feb 18: I gave an interview for the magazine Sciences et Avenir. Read the article here.
  • Feb 9: Our paper on "A Precision Medicine Initiative for Alzheimer's disease: the road ahead to biomarker-guided integrative disease modeling" has just been published in Climacteric!

Communications

Interview for Sciences&Avenir (02/2017)
Biovision conference, Lyon (04/2017)
Interview for the ICM (Brain and Spine Institute)(02/2016)
50th anniversary of INRIA (04/2017)
Interview for FrenchWeb.fr (05/2017)
France Inter (07/2017)

The team

Postdocs

PhD students

  • Thomas Lartigue (since 2017), co-supervised with S. Allassonnière
  • Raphael Couronné (since 2017)
  • Maxime Louis (since 2016)
  • Manon Ansart (since 2016), co-supervised with D. Dormont
  • Igor Koval (since 2016), co-supervised with S. Allassonnière
  • Alexandre Bône (since 2016), co-supervised with O. Colliot
  • Junhao Wen (since 2015), co-supervised with O. Colliot
  • Lou Albessard (since 2015), co-supervised with D. Grimaud-Hervé

Engineers and Scientists

  • Simona Bottani (since 2017), software engineer
  • Arnaud Marcoux (since 2017), imaging engineer
  • Sabrina Fontanella (since 2016), software developer
  • Michael Bacci (since 2016), software developer

Alumni

  • Jean-Baptiste Schiratti, PhD student (2013-2017), left for a joint postdoc position between A. Gramfort's lab at Telecom ParisTech and the start-up Bioserenity.
  • Barbara Gris, PhD student (2013-2016), left for a postdoc position in the mathematical department of KTH Stockholm with O. Oktem.
  • Pietro Gori, PhD student (2012 - 2016), left for a postdoc position at Neurospin in J.F. Mangin's lab.
  • Ana Beatriz Graciano Fouquier, postdoc (2013 - 2016), left for a R&D engineer position in the start-up Cardiawave.
  • Susovan Pal, postdoc (2014 - 2015), left for S. Joshi lab at UCLA
  • François Touvet, engineer (2013 - 2015), left for the 3D animation studio Ellipsanime
  • Alexandre Routier, engineer (2012 - 2015), left for a PhD at the Salpêtrière hospital

Publications

  • Editor of 4 archived conference proceedings (2 in the Springer LNCS series)
  • Author of more than 45 peer-reviewed publications (2/3 as first or last author), among which
    • journal articles in the highest ranked journals in the fields of neuroimaging (Neuroimage), image analysis (Medical Image Analysis, IEEE Trans. Medical Imaging, SIAM J. Imaging Sciences) and computer vision (International J. of Computer Vision)
    • articles in the most selective conferences in medical image analysis (Medical Image Computing and Computer-Assisted Intervention (MICCAI) and Information Processing in Medical Imaging (IPMI), among which 8 oral presentations with a selection rate below 5%) and statistical learning (Neural Information Processing System (NIPS))

Softwares

Deformetrica

Deformetrica is a collaborative project which provides cutting-edge statistical tools to analyze image and image-derived data with deformations. Input data may be images, curve- or surface- meshes in 2D or 3D. It can be used for:

  • Registration, namely the superimposition of images or geometric primitives by the computation of an optimal deformation
  • Atlas Construction, namely the estimation of an geometrical model from a series of example data, and summary of the variability in shape of this model across the samples

For more details, visit www.deformetrica.org


Exoshape

Developed within the European project Health-e-Child, the software ExoShape is a set of Matlab functions and Mex-files to perform statistical analysis of sets of curve and surface meshes. Its development was stopped in 2010, as the more ambitious Deformetrica project took over.

Want to support or join us?

Support us!

If you wish to support our research, you are welcome to donate to the Brain and Spine Institute (ICM), specifying that your donation is for supporting the research activities of the ARAMIS lab. Contact me for details.

If your company is looking for strong academic partnerships with a leading team in the field of geometric data analysis, feel free to contact me.

Join us!

If you are a brilliant master student or just graduated PhD (Congrats!) with a background in Electrical Engineering, Applied Mathematics or Computer Science, feel free to send me an Contact me (explaining me in 5 lines what you feel interesting in our research). Available positions include postdocs, PhD candidates and software engineers. Current open position are advertised here.