Emmanuel Emilien Louis Soubies

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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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

Emmanuel Emilien Louis Soubies

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

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

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

Adaptive Regularization For Three-Dimensional Optical Diffraction Tomography

Inner-Loop-Free ADMM for Cryo-EM

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

Dictionary Learning with Statistical Sparsity in the Presence of Noise

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

Pocket guide to solve inverse problems with GlobalBioIm

Optical diffraction tomography from single-molecule localization microscopy

Phaseless Diffraction Tomography With Regularized Beam Propagation

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

The Sliding Frank-Wolfe Algorithm for the BLASSO

Diffraction Tomography from Single-Molecule Localization Microscopy: Numerical Feasibility

User-Friendly Building of Reconstruction Algorithms with GlobalBioIm

User-Friendly Building of Reconstruction Algorithms for Solving Inverse Problems