Publications by Emmanuel Emilien Louis Soubies

Diffraction Tomography from Single-Molecule Localization Microscopy: Numerical Feasibility

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

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, Ferréol Arnaud Marie Soulez, Emmanuel Emilien Louis Soubies

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, Ahmed Ayoub, Joowon Lim, Emmanuel Emilien Louis Soubies, 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, Laurène Donati, Thanh-An Michel Pham, Emmanuel Emilien Louis Soubies

IEEE2020

Adaptive Regularization For Three-Dimensional Optical Diffraction Tomography

Michaël Unser, Demetri Psaltis, Thanh-An Michel Pham, Ahmed Ayoub, Emmanuel Emilien Louis Soubies, 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, Mona Zehni, Emmanuel Emilien Louis Soubies

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, Shayan Aziznejad, Emmanuel Emilien Louis Soubies

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

Sébastien Schaub, Emmanuel Emilien Louis Soubies

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

Closed-Form Expression of the Fourier Ring-Correlation for Single-Molecule Localization Microscopy

Michaël Unser, Daniel Sage, Thanh-An Michel Pham, Emmanuel Emilien Louis Soubies

Single-molecule localization microscopy (SMLM) is a popular microscopic technique that achieves super resolution imaging by localizing individual blinking molecules in thousands of frames. Therefore, the reconstructed high-resolution image is a combination ...

IEEE2019

The Sliding Frank-Wolfe Algorithm for the BLASSO

Emmanuel Emilien Louis Soubies, Quentin Alain Denoyelle, Gabriel Peyré

This paper showcases the Sliding Frank-Wolfe (SFW), which is a novel optimization algorithm to solve the BLASSO sparse spikes super-resolution problem. The BLASSO is the continuous (i.e. off-thegrid or grid-less) counterpart of the well-known `1 sparse reg ...

2019

Pocket guide to solve inverse problems with GlobalBioIm

Michaël Unser, Daniel Sage, Laurène Donati, Thanh-An Michel Pham, Ferréol Arnaud Marie Soulez, Michael Thompson McCann, Emmanuel Emilien Louis Soubies, Thomas Jean Debarre

GlobalBioIm is an open-source MATLAB (R) library for solving inverse problems. The library capitalizes on the strong commonalities between forward models to standardize the resolution of a wide range of imaging inverse problems. Endowed with an operator-al ...

2019

Computational Super-Sectioning for Single-Slice Structured-Illumination Microscopy

Michaël Unser, Emmanuel Emilien Louis Soubies

While structured-illumination microscopy (SIM) is inherently a three-dimensional (3-D) technique, many biological questions can be addressed from the acquisition of a single focal plane with high lateral resolution. Unfortunately, the single-slice reconstr ...

2019

Inner-Loop-Free ADMM for Cryo-EM

Michaël Unser, Laurène Donati, Emmanuel Emilien Louis Soubies

Thanks to recent advances in signal processing, the interest for fast ℓ1-regularized reconstruction algorithms in cryo-electron microscopy (cryo-EM) has intensified. The approaches based on the alternating-direction of multipliers method (ADMM) are particu ...

IEEE2019

Improving 3D MA-TIRF Reconstruction with Deconvolution and Background Estimation

Sébastien Schaub, Emmanuel Emilien Louis Soubies

Total internal reflection fluorescence microscopy (TIRF) produces 2D images of the fluorescent activity integrated over a very thin layer adjacent to the glass coverslip. By varying the illumination angle (multi-angle TIRF), a stack of 2D images is acquire ...

IEEE2019

Versatile reconstruction framework for diffraction tomography with intensity measurements and multiple scattering

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

2018

Phaseless Diffraction Tomography With Regularized Beam Propagation

Michaël Unser, Alexandre Goy, Demetri Psaltis, Thanh-An Michel Pham, Ferréol Arnaud Marie Soulez, Joowon Lim, Emmanuel Emilien Louis Soubies

In recent years, researchers have obtained impressive reconstructions of the refractive index (RI) of biological objects through the combined use of advanced physics (nonlinear forward model) and regularization. Here, we propose an adaptation of these tech ...

IEEE2018

GlobalBioIm: A Unifying Computational Framework for Solving Inverse Problems

Michaël Unser, Laurène Donati, Ferréol Arnaud Marie Soulez, Michael Thompson McCann, Emmanuel Emilien Louis Soubies

We present a unifying framework for the development of state-of-the-art reconstruction algorithms in computational optics with a clear separation between the physical (forward model) and signal-related (regularization, incorporation of prior constraints) a ...

OSA2017

Efficient Inversion of Multiple-Scattering Model for Optical Diffraction Tomography

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

Optical diffraction tomography relies on solving an inverse scattering problem governed by the wave equation. Classical reconstruction algorithms are based on linear approximations of the forward model (Born or Rytov), which limits their applicability to t ...

2017