Publications by Thanh-An Michel Pham

Phase Retrieval: From Computational Imaging to Machine Learning: A tutorial

Michaël Unser, Thanh-An Michel Pham, Jonathan Yuelin Dong

Phase retrieval consists in the recovery of a complex-valued signal from intensity-only measurements. As it pervades a broad variety of applications, many researchers have striven to develop phase-retrieval algorithms. Classical approaches involve techniqu ...

2023

Bayesian Inversion for Nonlinear Imaging Models Using Deep Generative Priors

Michaël Unser, Thanh-An Michel Pham, Pakshal Narendra Bohra, Jonathan Yuelin Dong

Most modern imaging systems incorporate a computational pipeline to infer the image of interest from acquired measurements. The Bayesian approach to solve such ill-posed inverse problems involves the characterization of the posterior distribution of the im ...

2022

Nonlinear Inverse Problems in Quantitative Phase Imaging

Thanh-An Michel Pham

The topic of this thesis is the development of new algorithmic reconstruction methods for quantitative phase imaging (QPI). In the past decade, advanced QPI has emerged as a valuable tool to study label-free biological samples and uncover their 3D structur ...

EPFL2022

Mechanical artifacts in optical projection tomography: classification and automatic calibration

Michaël Unser, Thanh-An Michel Pham, François Thierry M Marelli, Jonathan Yuelin Dong

Optical projection tomography (OPT) is a powerful tool for biomedical studies. It achieves 3D visualization of mesoscopic biological samples with high spatial resolution using conventional tomographic-reconstruction algorithms. However, various artifacts d ...

Optica Publishing Group2022

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

Robust Phase Unwrapping via Deep Image Prior for Quantitative Phase Imaging

Matthias Lütolf, Michaël Unser, Nathalie Brandenberg, Thanh-An Michel Pham, Fangshu Yang

Quantitative phase imaging (QPI) is an emerging label-free technique that produces images containing morphological and dynamical information without contrast agents. Unfortunately, the phase is wrapped in most imaging system. Phase unwrapping is the comput ...

2021

Optimal-Transport-Based Metric for SMLM

Michaël Unser, Daniel Sage, Thanh-An Michel Pham, Quentin Alain Denoyelle, Pol del Aguila Pla

We propose the use of Flat Metric to assess the performance of reconstruction methods for single-molecule localization microscopy (SMLM) in scenarios where the ground-truth is available. Flat Metric is intimately related to the concept of optimal transport ...

IEEE2021

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

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

A method for assessing the fidelity of optical diffraction tomography reconstruction methods using structured illumination

Michaël Unser, Demetri Psaltis, Thanh-An Michel Pham, Ahmed Ayoub, Joowon Lim

2020

Deep-learning projector for optical diffraction tomography

Michaël Unser, Thanh-An Michel Pham, Harshit Gupta, Fangshu Yang

Optical diffraction tomography is an effective tool to estimate the refractive indices of unknown objects. It proceeds by solving an ill-posed inverse problem for which the wave equation governs the scattering events. The solution has traditionally been de ...

2020

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

Super-resolution fight club: assessment of 2D and 3D single-molecule localization microscopy software

Michaël Unser, Daniel Sage, Ricardo Henriques, Thanh-An Michel Pham, Thomas Pengo, Seamus John Holden, Tomas Lukes, Anna Archetti, Silvia Colabrese, Anurag Agrawal

With the widespread uptake of two-dimensional (2D) and three-dimensional (3D) single-molecule localization microscopy (SMLM), a large set of different data analysis packages have been developed to generate super-resolution images. In a large community effo ...

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

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

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

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