Publications by Emmanuel Emilien Louis Soubies

Diffraction Tomography from Single-Molecule Localization Microscopy: Numerical Feasibility

Michaël Unser, Thanh-An Michel Pham, Emmanuel Emilien Louis Soubies, Ferréol Arnaud Marie Soulez

Single-molecule localization microscopy (SMLM) is a fluorescence microscopy technique that achieves super-resolution imaging by sequentially activating and localizing random sparse subsets of fluorophores. Each activated fluorophore emits light that then s ...

IEEE2021

Optical diffraction tomography from single-molecule localization microscopy

Michaël Unser, Thanh-An Michel Pham, Emmanuel Emilien Louis Soubies, Ferréol Arnaud Marie Soulez

Single-molecule localization microscopy (SMLM) is a powerful method for the imaging of cellular structures. This modality delivers nanoscale resolution by sequentially activating a subset of fluorescent molecules and by extracting their super-resolved posi ...

2021

Three-Dimensional Optical Diffraction Tomography With Lippmann-Schwinger Model

Michaël Unser, Demetri Psaltis, Thanh-An Michel Pham, Emmanuel Emilien Louis Soubies, Joowon Lim, Ahmed Ayoub, Ahmed Bassam Sayed Ayoub Mohamed Emam

A broad class of imaging modalities involve the resolution of an inverse-scattering problem. Among them, three-dimensional optical diffraction tomography (ODT) comes with its own challenges. These include a limited range of views, a large size of the sampl ...

2020

User-Friendly Building of Reconstruction Algorithms with GlobalBioIm

Michaël Unser, Laurène Donati, Emmanuel Emilien Louis Soubies

2020

User-Friendly Building of Reconstruction Algorithms for Solving Inverse Problems

Michaël Unser, Thanh-An Michel Pham, Laurène Donati, Emmanuel Emilien Louis Soubies

IEEE2020

Adaptive Regularization For Three-Dimensional Optical Diffraction Tomography

Michaël Unser, Demetri Psaltis, Thanh-An Michel Pham, Emmanuel Emilien Louis Soubies, Ahmed Ayoub, Ahmed Bassam Sayed Ayoub Mohamed Emam

Optical diffraction tomography (ODT) allows one to quantitatively measure the distribution of the refractive index of the sample. It relies on the resolution of an inverse scattering problem. Due to the limited range of views as well as optical aberrations ...

IEEE2020

Joint Angular Refinement and Reconstruction for Single-Particle Cryo-EM

Michaël Unser, Laurène Donati, Emmanuel Emilien Louis Soubies, Mona Zehni

Single-particle cryo-electron microscopy (cryo-EM) reconstructs the three-dimensional (3D) structure of bio-molecules from a large set of 2D projection images with random and unknown orientations. A crucial step in the single-particle cryo-EM pipeline is 3 ...

2020

The sliding Frank-Wolfe algorithm and its application to super-resolution microscopy

Emmanuel Emilien Louis Soubies, Quentin Alain Denoyelle, Gabriel Peyré

This paper showcases the theoretical and numerical performance of the Sliding Frank-Wolfe, which is a novel optimization algorithm to solve the BLASSO sparse spikes super-resolution problem. The BLASSO is a continuous (i.e. off-the-grid or grid-less) count ...

2020

Dictionary Learning with Statistical Sparsity in the Presence of Noise

Michaël Unser, Emmanuel Emilien Louis Soubies, Shayan Aziznejad

We consider a new stochastic formulation of sparse representations that is based on the family of symmetric alpha-stable (S alpha S) distributions. Within this framework, we develop a novel dictionary-learning algorithm that involves a new estimation techn ...

IEEE2020

Nanometric axial resolution of fibronectin assembly units achieved with an efficient reconstruction approach for multi-angle-TIRF microscopy

Emmanuel Emilien Louis Soubies, Sébastien Schaub

High resolution imaging of molecules at the cell-substrate interface is required for understanding key biological processes. Here we propose a complete pipeline for multi-angle total internal reflection fluorescence microscopy (MA-TIRF) going from instrume ...

Nature Research2019