Emmanuel Soubies

Postdoctoral Researcher at EPFL, Biomedical Imaging Group

Journals

2018 Versatile Reconstruction Framework for Diffraction Tomography with Intensity Measurements and Multiple Scattering, Optics Express, 26-3, pp. 2749-2763, 2018.
Thanh-An Pham, Emmanuel Soubies, Joowon Lim, Alexandre Goy, Ferréol Soulez, Demetri Psaltis and Michael Unser. [Hal] [Journal]
2017

Efficient Inversion of Multiple-Scattering Model for Optical Diffraction Tomography
Optics Express 25-18, pp. 21786-21800, 2017 (Editors' Pick).
Emmanuel Soubies, Thanh-An Pham and Michael Unser. [arXiv] [Journal] [Code]

A Unified View of Exact Continuous Penalties for l2-l0 Minimization.
SIAM Journal on Optimization 27-3, pp. 2034-2060, 2017.
Emmanuel Soubies, Laure Blanc-Féraud and Gilles Aubert. [Hal]

2015 A Continuous Exact l0 Penalty (CEL0) for Least-Squares Regularized Problem.
SIAM Journal on Imaging Science 8-3, pp. 1574-1606, 2015.
Emmanuel Soubies, Laure Blanc-Féraud and Gilles Aubert. [Hal] [Erratum]

Conferences

2018 Phaseless Diffraction Tomography with Regularized Beam Propagation. Proc. ISBI.
Thanh-An Pham, Emmanuel Soubies, Joowon Lim, Alexandre Goy, Ferréol Soulez, Demetri Psaltis and Michael Unser. [pdf]
2017

Quelles Relaxations Continues pour le Critère l2-l0? Colloque GRETSI.
Emmanuel Soubies, Laure Blanc-Féraud and Gilles Aubert. [Hal]

GlobalBioIm: A Unifying Computational Framework for Solving Inverse Problems. Proc. COSI.
Michael Unser, Emmanuel Soubies, Ferréol Soulez, Michael McCann and Laurène Donati. [pdf] [Website]

Sparse Super-Resolution from Laplace Measurements. SPARS.
Quentin Denoyelle, Emmanuel Soubies, Vincent Duval and Gabriel Peyré. [pdf]

High Density Molecule Localization for Super-Resolution Microscopy Using CEL0 Based Sparse Approximation. Proc. ISBI.
Simon Gazagnes, Emmanuel Soubies and Laure Blanc-Féraud. [Hal] [Code]

2016

A Framework for Multi-Angle TIRF Microscope Calibration. Proc. ISBI.
Emmanuel Soubies, Sébastien Schaub, Agata Radwanska, Ellen Van Obberghen-Schilling, Laure Blanc-Féraud and Gilles Aubert. [Hal]

2015

L0-Optimization for Channel and DOA Sparse Estimation. Proc. CAMSAP.
Adilson Chinatto, Emmanuel Soubies, Cynthia Junqueira, João M. T. Romano, Pascal Larzabal, Jean-Pierre Barbot and Laure Blanc-Féraud. [Hal]

Seuillage CEL0 pour la Minimisation l2-l0 : Comparaisons avec IHT. Colloque GRETSI.
Emmanuel Soubies, Laure Blanc-Féraud and Gilles Aubert. [Hal]

CEL0: A Continuous Alternative to l0 Penalty. SPARS.
Emmanuel Soubies, Laure Blanc-Féraud and Gilles Aubert. [Hal]

Cells Detection Using Segmentation Competition. Proc. ISBI.
Emmanuelle Poulain, Sylvain Prigent, Emmanuel Soubies and Xavier Descombes. [Hal]

2014

Sparse Reconstruction from Multi-Angle TIRF Microscopy. Proc ICIP.
Emmanuel Soubies, Laure Blanc-Féraud, Sébastien Schaub and Gilles Aubert. [Hal]

A 3D Model with Shape Prior Information for Biological Structures Reconstruction using Multiple-Angle Total Internal Reflection Fluorescence Microscopy. Proc. ISBI.
Emmanuel Soubies, Laure Blanc-Féraud, Sébastien Schaub and Gilles Aubert. [Hal]

2013

A 3D Segmentation Algorithm for Ellipsoidal Shapes. Application to Nuclei Extraction. Proc. ICPRAM. Emmanuel Soubies, Pierre Weiss and Xavier Descombes. [Hal]

Book sections

2015

Graph-Cut Based Segmentation of Predefined Shapes: Applications to Biological Imaging.
In Pattern Recognition Applications and Methods. A. Fred and M. De Marisco (eds.), Springer, 2015.
Emmanuel Soubies, Pierre Weiss and Xavier Descombes. (Revised Selected Papers ICPRAM 2013) [pdf]

Thesis

2016

Sur Quelques Problèmes de Reconstruction en Imagerie MA-TIRF et en Optimisation Parcimonieuse par Relaxation Continue Exacte de Critères Pénalisés en Norme-l0. PhD Thesis, Université Nice Sophia-Antipolis, October 2016. [Manuscript]

Invited Talks

  • Journées MAS, August 2018, Dijon (France):
       Super-résolution en microscopie.
  • OSA Imaging and Applied Optics Congress on Mathematics in Imaging, June 2018, Orlando (USA):
       Splitting Based Methods for Structured Illumination Microscopy.
  • SIAM Conference on Imaging Science, June 2018, Bologna (Italy):
       Exact continuous relaxations for the l0-regularized least-squares criteria.
  • MIA conference, January 2018, Berlin (Germany):
       On a class of exact continuous relaxations of the l2-l0 criteria.
  • Seminar Télécom Paristech, November 2017, Paris (France):
       Exact continuous relaxations for the l0-regularized least-squares criteria.
  • Seminar IMB, November 2017, Bordeaux (France):
       Exact continuous relaxations for the l0-regularized least-squares criteria.
  • Seminar LS2N, October 2017, Nantes (France):
       Exact continuous relaxations for the l0-regularized least-squares criteria.
  • Seminar IRIT, October 2017, Toulouse (France):
       Exact continuous relaxations for the l0-regularized least-squares criteria.
  • Workshop Dictionary Learning on Manifolds, September 2017, Nice (France):
       Dictionary Learning Based on Sparse Distribution Tomography for 3D Deconvolution Microscopy.
  • Congrès SMAI, June 2017, Ronce les Bains (France):
       Vers une vue unifiée des relaxations continues exactes du critère l2-l0.
  • Seminar Biomedical Imaging Group , May 2016, EPFL, Lausanne (Switzerland):
       Some results on MA-TIRF reconstruction and exact continuous penalties for l2-l0 minimization..
  • SMATI (joint seminar between MAP5 and LTCI), December 2015, LTCI, Paris (France):
       The Continuous Exact l0 penalty: An alternative to l0-norm.
  • Séminaires signal - apprentissage, November 2015, CMI, Marseille (France):
       The Continuous Exact l0 penalty: An alternative to l0-norm.
  • Workshop Axe Physique du Vivant de l'UNS, September 2015, Nice (France):
       High resolution imaging using Multi-Angle TIRF microscopy.
  • MICA Days, December 2014, Nice (France):
       From single TIRF to Multiple-Angle TIRF. How to improve axial resolution.

Emmanuel Soubies - 2014