Publications by Laurène Donati

A Practical Guide to Supervised Deep Learning for Bioimage Analysis: Challenges and good practices

Daniel Sage, Laurène Donati, Virginie Sophie Uhlmann

The variety of bioimage data and their quality have dramatically increased over the last decade. In parallel, the number of proposed deep learning (DL) models for their analysis grows by the day. Yet, the adequate reuse of published tools by practitioners ...

IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC2022

CryoGAN: A New Reconstruction Paradigm for Single-Particle Cryo-EM Via Deep Adversarial Learning

Michaël Unser, Laurène Donati, Harshit Gupta, Michael Thompson McCann

We present CryoGAN, a new paradigm for single-particle cryo-electron microscopy (cryo-EM) reconstruction based on unsupervised deep adversarial learning. In single-particle cryo-EM, the structure of a biomolecule needs to be reconstructed from a large set ...

2021

DeepImageJ: A user-friendly environment to run deep learning models in ImageJ

Michaël Unser, Daniel Sage, Laurène Donati

DeepImageJ offers a user-friendly solution in ImageJ to run trained deep learning models for biomedical image analysis. It includes guiding tools for reliable analyses, contributing to the democratization of deep learning in microscopy. ...

NATURE PORTFOLIO2021

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

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

Reconstruction Methods for Cryo-Electron Microscopy: From Model-based to Data-driven

Laurène Donati

The topic of this thesis is the development of new reconstruction methods for cryo-electron microscopy (cryo-EM). Cryo-EM has revolutionized the field of structural biology over the last decade and now permits the regular discovery of biostructures. Yet, t ...

EPFL2020

Pocket guide to solve inverse problems with GlobalBioIm

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

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

Fast multiscale reconstruction for Cryo-EM

Michaël Unser, Laurène Donati, Masih Nilchian

We present a multiscale reconstruction framework for single-particle analysis (SPA). The representation of three-dimensional (3D) objects with scaled basis functions permits the reconstruction of volumes at any desired scale in the real-space. This multisc ...

Elsevier2018