Publications by François Aguet

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This thesis introduces a collection of physics-based methods for super-resolution in optical microscopy. The core of these methods constitutes a framework for 3-D localization of single fluorescent molecules. Localization is formulated as a parameter estim ...

With the recent development of fluorescent probes and new high-resolution microscopes, biological imaging has entered a new era and is presently having a profound impact on the way research is being conducted in the life sciences. Biologists have come to d ...

Fluorophores that are fixed during image acquisition produce a diffraction pattern that is characteristic of the orientation of the fluorophore’s underlying dipole. Fluorescence localization microscopy techniques such as PALM and STORM achieve super-resolu ...

We construct parametric active contours (snakes) for outlining cells in histology images. These snakes are defined in terms of cubic B-spline basis functions. We use a steerable ridge detector for obtaining a reliable map of the cell boundaries. Using the ...

Due to the limited depth of field of brightfield microscopes, it is usually impossible to image thick specimens entirely in focus. By optically sectioning the specimen, the in-focus information at the specimen's surface can be acquired over a range of imag ...

Localization microscopy relies on computationally efficient Gaussian approximations of the point spread function for the calculation of fluorophore positions. Theoretical predictions show that under specific experimental conditions, localization accuracy i ...

This paper addresses the problem of reconstructing an image from 1-bit-quantized measurements, considering a simple but nonconventional optical acquisition model. Following a compressed-sensing design, a known pseudo-random phase-shifting mask is introduce ...

Brightfield microscopy often suffers from limited depth of field, which prevents thick specimens from being imaged entirely in-focus. By optically sectioning the specimen, the in-focus regions can be acquired over multiple images. Extended depth of field m ...

One of the ongoing challenges in single particle fluorescence microscopy resides in estimating the axial position of particles with sub-resolution precision. Due to the complexity of the diffraction patterns generated by such particles, the standard fittin ...

Most state-of-the-art algorithms for filament detection in 3-D image-stacks rely on computing the Hessian matrix around individual pixels and labeling these pixels according to its eigenvalues. This approach, while very effective for clean data, hi which linear structures are nearly cylindrical, loses its effectiveness in the presence of noisy data and irregular structures.

State-of-the-art approaches to detecting ridge-like structures in images rely on filters designed to respond to locally linear intensity features. While these approaches may be optimal for ridges whose appearance is close to being ideal, their performance degrades quickly in the presence of structured noise that corrupts the image signal, potentially to the point where it truly does not conform to the ideal model anymore. In this paper, we address this issue by introducing a learning framework that relies o

We present a framework for feature detection in 3-D using steerable filters. These filters can be designed to optimally respond to a particular type of feature by maximizing several Canny-like criteria. The detection process involves the analytical computa ...

François Aguet

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Super-resolution fluorescence microscopy based on physical models

The Colored Revolution of Bioimaging

Super-resolution orientation estimation and localization of fluorescent dipoles using 3-D steerable filters

Parametric B-Spline Snakes on Distance Maps—Application to Segmentation of Histology Images

Model-Based 2.5-D Deconvolution for Extended Depth of Field in Brightfield Microscopy

3-D PSF fitting for fluorescence microscopy: implementation and localization application

Optical Imaging Using Binary Sensors

Joint Texture and Topography Estimation for Extended Depth of Field in Brightfield Microscopy

A Maximum-Likelihood Formalism for Sub-Resolution Axial Localization of Fluorescent Nanoparticles

Steerable Features for Statistical 3D Dendrite Detection

Rotational Features Extraction for Ridge Detection

Sub-Resolution Axial Localization of Nanoparticles in Fluorescence Microscopy

Three-Dimensional Feature Detection Using Optimal Steerable Filters