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Virginie Sophie Uhlmann

Cette personne a quitté l’EPFL

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Publications associées (24)

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Multimodal imaging and high-throughput image-processing for drug screening on living organisms on-chip

Michaël Unser, Martinus Adela Maria Gijs, Johan Auwerx, Matteo Cornaglia, Laurent Mouchiroud, Daniel Migliozzi, Virginie Sophie Uhlmann

A major step for the validation of medical drugs is the screening on whole organisms, which gives the systemic information that is missing when using cellular models. Caenorhabditis elegans is a soil worm that catches the interest of researchers who study ...

SPIE Society of Photo-optical Instrumentation Engineers2019

Multiresolution Subdivision Snakes

Michaël Unser, Daniel Andreas Schmitter, Virginie Sophie Uhlmann, Anaïs Laure Marie-Thérèse Badoual

We present a new family of snakes that satisfy the property of multiresolution by exploiting subdivision schemes. We show in a generic way how to construct such snakes based on an admissible subdivision mask. We derive the necessary energy formulations and ...

2017

Dictionary Learning for Two-Dimensional Kendall Shapes

Michaël Unser, Julien René Fageot, Virginie Sophie Uhlmann

We propose a novel sparse dictionary learning method for planar shapes in the sense of Kendall, namely configurations of landmarks in the plane considered up to similitudes. Our shape dictionary method provides a good trade-off between algorithmic simplici ...

SIAM PUBLICATIONS2020

Landmark Active Contours for Bioimage Analysis : A Tale of Points and Curves

Virginie Sophie Uhlmann

The problem of identifying the outline of objects in images can be approached from two starting points, either by considering localized features (landmarks, keypoints or regions), or by searching for global contours. Features are regions or points of int ...

EPFL2017

General Surface Energy for Spinal Cord and Aorta Segmentation

Michaël Unser, Daniel Andreas Schmitter, Virginie Sophie Uhlmann, Harshit Gupta

We present a new surface energy potential for the segmentation of cylindrical objects in 3D medical imaging using parametric spline active contours (a.k.a. spline-snakes). Our energy formulation is based on an optimal steerable surface detector. Thus, we c ...

IEEE2017

Statistical Optimality of Hermite Splines

Michaël Unser, Julien René Fageot, Virginie Sophie Uhlmann, Harshit Gupta

Hermite splines are commonly used for interpolating data when samples of the derivative are available, in a scheme called Hermite interpolation. Assuming a suitable statistical model, we demonstrate that this method is actually optimal for reconstructing r ...

IEEE2015

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

Daniel Sage, Virginie Sophie Uhlmann, Laurène Donati

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

CP-CHARM: Segmentation-Free Image Classification Made Accessible

Virginie Sophie Uhlmann

Background: Automated classification using machine learning often relies on features derived from segmenting individual objects, which can be difficult to automate. WND-CHARM is a previously developed classification algorithm in which features are computed ...

2016

Gaussian and sparse processes are limits of generalized Poisson processes

Michaël Unser, Julien René Fageot, Virginie Sophie Uhlmann

The theory of sparse stochastic processes offers a broad class of statistical models to study signals, far beyond the more classical class of Gaussian processes. In this framework, signals are represented as realizations of random processes that are soluti ...

2020

Support and approximation properties of Hermite splines

Michaël Unser, Julien René Fageot, Shayan Aziznejad, Virginie Sophie Uhlmann

In this paper, we formally investigate two mathematical aspects of Hermite splines that are relevant to practical applications. We first demonstrate that Hermite splines are maximally localized, in the sense that the size of their support is minimal among ...

2020

Efficient Shape Priors for Spline-Based Snakes

Michaël Unser, Daniel Andreas Schmitter, Ricard Delgado Gonzalo, Virginie Sophie Uhlmann

Parametric active contours are an attractive approach for image segmentation, thanks to their computational efficiency. They are driven by application-dependent energies that reflect the prior knowledge on the object to be segmented. We propose an energy i ...

2015

Design of Steerable Wavelets to Detect Multifold Junctions

Michaël Unser, Cédric René Jean Vonesch, Virginie Sophie Uhlmann, Zsuzsanna Püspöki

We propose a framework for the detection of junctions in images. Although the detection of edges and key points is a well examined and described area, the multiscale detection of junction centers, especially for odd orders, poses a challenge in pattern ana ...

IEEE2015

Snakes with Tangent-Based Control and Energies for Bioimage Analysis

Michaël Unser, Ricard Delgado Gonzalo, Virginie Sophie Uhlmann

We propose a novel active contour for the analysis of filament-like structures and boundaries—features that traditional snakes based on closed curves have difficulties to delineate. Our method relies on a parametric representation of an open curve involvin ...

IEEE2014

FlyLimbTracker: An Active Contour Based Approach for Leg Segment Tracking in Unmarked, Freely Behaving Drosophila

Michaël Unser, Ricard Delgado Gonzalo, Virginie Sophie Uhlmann

Understanding the biological underpinnings of movement and action requires the development of tools for quantitative measurements of animal behavior. Drosophila melanogaster provides an ideal model for developing such tools: the fly has unparalleled geneti ...

2017

Supervised learning to quantify amyloidosis in whole brains of an Alzheimer's disease mouse model acquired with optical projection tomography

Dimitri Nestor Alice Van De Ville, Theo Lasser, Aleksandra Radenovic, Virginie Sophie Uhlmann, Paul James Marchand, David Nguyen, Arielle Louise Planchette

Alzheimer's disease (AD) is characterized by amyloidosis of brain tissues. This phenomenon is studied with genetically-modified mouse models. We propose a method to quantify amyloidosis in whole 5xFAD mouse brains, a model of AD. We use optical projection ...

2019

User-Friendly Image-Based Segmentation and Analysis of Chromosomes

Michaël Unser, Florian Maria Wurm, Lucia Baldi Unser, Ricard Delgado Gonzalo, Virginie Sophie Uhlmann

We designed two efficient and user-friendly tools for the segmentation and analysis of images containing chromosomes or, more generally, rod-shaped elements that are spread on microscopic slides. The segmentation tool allows to automatically extract the pr ...

IEEE2016

VOW: Variance-Optimal Wavelets for the Steerable Pyramid

Michaël Unser, Virginie Sophie Uhlmann, Pedram Pad

We study the issue of localization in the context of isotropic wavelet frames. We define a variance-type measure of localization and propose an algorithm based on calculus of variations to minimize this criterion under the constraint of a tight wavelet fra ...

IEEE2014

Diverse M-Best Solutions by Dynamic Programming

Michaël Unser, Virginie Sophie Uhlmann

Many computer vision pipelines involve dynamic programming primitives such as finding a shortest path or the minimum energy solution in a tree-shaped probabilistic graphical model. In such cases, extracting not merely the best, but the set of M-best soluti ...

Springer2017

Maximally Localized Radial Profiles for Tight Steerable Wavelet Frames

Michaël Unser, Virginie Sophie Uhlmann, Pedram Pad

A crucial component of steerable wavelets is the radial profile of the generating function in the frequency domain. In this paper, we present an infinite-dimensional optimization scheme that helps us find the optimal profile for a given criterion over the ...

IEEE2016

Exponential Hermite Splines For The Analysis Of Biomedical Images

Michaël Unser, Ricard Delgado Gonzalo, Virginie Sophie Uhlmann

We present a new exponential B-spline basis that enables the construction of active contours for the analysis of biomedical images. Our functions generalize the well-known polynomial Hermite B-splines and provide us with a direct control over the tangents ...

Ieee2014