Jean-Philippe Thiran

Jean-Philippe Thiran
École Polytechnique Fédérale de Lausanne | EPFL · Signal Processing Laboratory

Professor

About

963
Publications
126,210
Reads
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28,124
Citations
Citations since 2016
358 Research Items
15057 Citations
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Introduction
Jean-Philippe Thiran was born in Namur, Belgium, in August 1970. He received the Electrical Engineering degree and the PhD degree from the Université catholique de Louvain (UCL), Louvain-la-Neuve, Belgium, in 1993 and 1997, respectively. Dr Thiran is a full professor at EPFL, director of the Signal Processing Lab. He also holds a 20% associate professor position with the Department of Radiology of the University Hospital Center and University of Lausanne (CHUV-UNIL).

Publications

Publications (963)
Article
Full-text available
Enhanced behavioral interventions are gaining increasing interest as innovative treatment strategies for major depressive disorder (MDD). In this study protocol, we propose to examine the synergistic effects of a self-administered home-treatment, encompassing transcranial direct current stimulation (tDCS) along with a video game based training of a...
Chapter
Computer-aided clinical decision support tools for radiology often suffer from poor generalizability in multi-centric frameworks due to data heterogeneity. In particular, magnetic resonance images depend on a large number of acquisition protocol parameters as well as hardware and software characteristics that might differ between or even within ins...
Article
Full-text available
Despite recent improvements, complete motor recovery occurs in <15% of stroke patients. To improve the therapeutic outcomes, there is a strong need to tailor treatments to each individual patient. However, there is a lack of knowledge concerning the precise neuronal mechanisms underlying the degree and course of motor recovery and its individual di...
Preprint
Full-text available
In a companion paper, a faceted wideband imaging technique for radio interferometry, dubbed Faceted HyperSARA, has been introduced and validated on synthetic data. Building on the recent HyperSARA approach, Faceted HyperSARA leverages the splitting functionality inherent to the underlying primal-dual forward-backward algorithm to decompose the imag...
Preprint
Full-text available
Diffusion-weighted magnetic resonance imaging (DW-MRI) is used to characterize brain tissue microstructure employing tissue-specific biophysical models. A current limitation, however, is that most of the proposed models are based on the assumption of negligible water exchange between the intra- and extracellular compartments, which might not be val...
Article
Full-text available
Limitations in the accuracy of brain pathways reconstructed by diffusion MRI (dMRI) tractography have received considerable attention. While the technical advances spearheaded by the Human Connectome Project (HCP) led to significant improvements in dMRI data quality, it remains unclear how these data should be analyzed to maximize tractography accu...
Conference Paper
Flow is a mental state experienced during holistic involvement in a certain task, and it is a factor that promotes motivation, development, and performance. A reliable and objective estimation of the flow is essential for moving away from the traditional self-reporting subjective questionnaires, and for developing closed-loop human-computer interfa...
Article
Full-text available
Computer-aided diagnostics in histopathology are based on the digitization of glass slides. However, heterogeneity between the images generated by different slide scanners can unfavorably affect the performance of computational algorithms. Here, we evaluate the impact of scanner variability on lymph node segmentation due to its clinical importance...
Article
Full-text available
Quantitative magnetic resonance imaging (qMRI) can increase the specificity and sensitivity of conventional weighted MRI to underlying pathology by comparing meaningful physical or chemical parameters, measured in physical units, with normative values acquired in a healthy population. This study focuses on multi-echo T2 relaxometry, a qMRI techniqu...
Article
Tractography enables identifying and evaluating the healthy and diseased brain's white matter pathways from diffusion-weighted magnetic resonance imaging data. As previous evaluation studies have reported significant false-positive estimation biases, recent microstructure-informed tractography algorithms have been introduced to improve the trade-of...
Article
Supervised learning is constrained by the availability of labeled data, which are especially expensive to acquire in the field of digital pathology. Making use of open-source data for pre-training or using domain adaptation can be a way to overcome this issue. However, pre-trained networks often fail to generalize to new test domains that are not d...
Article
Full-text available
This paper describes the development of a novel medical x-ray imaging system adapted to the needs and constraints of low- and middle-income countries. The developed system is based on an indirect conversion chain: a scintillator plate produces visible light when excited by the x rays, and then, a calibrated multi-camera architecture converts the vi...
Preprint
Full-text available
Manually segmenting multiple sclerosis (MS) cortical lesions (CL) is extremely time-consuming, and past studies have shown only moderate inter-rater reliability. To accelerate this task, we developed a deep learning-based framework (CLAIMS: Cortical Lesion Artificial Intelligence-based assessment in Multiple Sclerosis) for the automated detection a...
Article
Full-text available
Manually segmenting multiple sclerosis (MS) cortical lesions (CL) is extremely time‐consuming, and past studies have shown only moderate inter‐rater reliability. To accelerate this task, we developed a deep learning‐based framework (CLAIMS: Cortical Lesion Artificial Intelligence‐based assessment in Multiple Sclerosis) for the automated detection a...
Preprint
Full-text available
Progress in digital pathology is hindered by high-resolution images and the prohibitive cost of exhaustive localized annotations. The commonly used paradigm to categorize pathology images is patch-based processing, which often incorporates multiple instance learning (MIL) to aggregate local patch-level representations yielding image-level predictio...
Preprint
Full-text available
Purpose: To investigate aspects of the validation of self-supervised algorithms for reconstruction of undersampled MR images: quantitative evaluation of prospective reconstructions, potential differences between prospective and retrospective reconstructions, suitability of commonly used quantitative metrics, and generalizability. Theory and Methods...
Preprint
Full-text available
The current multiple sclerosis (MS) diagnostic criteria lack specificity, and this may lead to misdiagnosis, which remains an issue in present-day clinical practice. In addition, conventional biomarkers only moderately correlate with MS disease progression. Recently, advanced MS lesional imaging biomarkers such as cortical lesions (CL), the central...
Article
Long acquisition times preclude the application of multiecho spin echo (MESE) sequences for myelin water fraction (MWF) mapping in daily clinical practice. In search of alternative methods, previous studies of interest explored the biophysical modeling of MWF from measurements of different tissue properties that can be obtained in scan times shorte...
Preprint
Full-text available
Limitations in the accuracy of brain pathways reconstructed by diffusion MRI (dMRI) tractography have received considerable attention. While the technical advances spearheaded by the Human Connectome Project (HCP) led to significant improvements in dMRI data quality, it remains unclear how these data should be analyzed to maximize tractography accu...
Article
Full-text available
Introduction Cervical cancer remains a major public health challenge in low- and middle-income countries (LMICs) due to financial and logistical issues. WHO recommendation for cervical cancer screening in LMICs includes HPV testing as primary screening followed by visual inspection with acetic acid (VIA) and treatment. However, VIA is a subjective...
Article
Ultrafast ultrasound (US) revolutionized biomedical imaging with its capability of acquiring full-view frames at over 1 kHz, unlocking breakthrough modalities such as shear-wave elastography and functional US neuroimaging. Yet, it suffers from strong diffraction artifacts, mainly caused by grating lobes, sidelobes, or edge waves. Multiple acquisiti...
Preprint
Full-text available
Background: The World Health Organization (WHO) recommendations for promoting effective management of cervical cancer screening in low- and medium-income countries (LMIC) include human papillomavirus (HPV) testing as primary screening followed by visual inspection with acetic acid (VIA) and, if required, treatment. The application of acetic acid in...
Article
Full-text available
White matter bundle segmentation using diffusion MRI fiber tractography has become the method of choice to identify white matter fiber pathways in vivo in human brains. However, like other analyses of complex data, there is considerable variability in segmentation protocols and techniques. This can result in different reconstructions of the same in...
Article
In magnetic resonance imaging, the application of a strong diffusion weighting suppresses the signal contributions from the less diffusion-restricted constituents of the brain's white matter, thus enabling the estimation of the transverse relaxation time T2 that arises from the more diffusion-restricted constituents such as the axons. However, the...
Preprint
The spatial impulse response (SIR) method is a well-known approach to calculate transient acoustic fields of arbitrary-shape transducers. It involves the evaluation of a time-dependent surface integral. Although analytic expressions of the SIR exist for some geometries, numerical methods based on the discretization of transducer surfaces have becom...
Preprint
Full-text available
In medical image segmentation, supervised deep networks' success comes at the cost of requiring abundant labeled data. While asking domain experts to annotate only one or a few of the cohort's images is feasible, annotating all available images is impractical. This issue is further exacerbated when pre-trained deep networks are exposed to a new ima...
Article
Cancer diagnosis, prognosis, and therapy response predictions from tissue specimens highly depend on the phenotype and topological distribution of constituting histological entities. Thus, adequate tissue representations for encoding histological entities is imperative for computer aided cancer patient care. To this end, several approaches have lev...
Chapter
Segmenting histology images into diagnostically relevant regions is imperative to support timely and reliable decisions by pathologists. To this end, computer-aided techniques have been proposed to delineate relevant regions in scanned histology slides. However, the techniques necessitate task-specific large datasets of annotated pixels, which is t...
Article
Multi-echo T2 magnetic resonance images contain information about the distribution of T2 relaxation times of compartmentalized water, from which we can estimate relevant brain tissue properties such as the myelin water fraction (MWF). Regularized non-negative least squares (NNLS) is the tool of choice for estimating non-parametric T2 spectra. Howev...
Chapter
Full-text available
We present a detailed description of the structural characteristics of the MICCAI 2021 Diffusion Simulated Connectivity (DiSCo) Challenge synthetic dataset. The DiSCo dataset are one of a kind numerical phantoms for the simulation of the diffusion-weighted images (DWIs) via Monte-Carlo diffusion simulations. The microscopic and macroscopic complexi...
Article
Full-text available
The methodological development in the mapping of the brain structural connectome from diffusion-weighted magnetic resonance imaging (DW-MRI) has raised many hopes in the neuroscientific community. Indeed, the knowledge of the connections between different brain regions is fundamental to study brain anatomy and function. The reliability of the struc...
Preprint
Full-text available
Supervised learning is constrained by the availability of labeled data, which are especially expensive to acquire in the field of digital pathology. Making use of open-source data for pre-training or using domain adaptation can be a way to overcome this issue. However, pre-trained networks often fail to generalize to new test domains that are not d...
Preprint
Full-text available
In magnetic resonance imaging, the application of a strong diffusion weighting suppresses the signal contributions from the less diffusion-restricted constituents of the brain's white matter, thus enabling the estimation of the transverse relaxation time T2 that arises from the more diffusion-restricted constituents such as the axons. However, the...
Article
Full-text available
We present the comparison of two-dimensional (2D) fetal brain biometry on magnetic resonance (MR) images using orthogonal 2D T2-weighted sequences (T2WSs) vs. one 3D super-resolution (SR) reconstructed volume and evaluation of the level of confidence and concordance between an experienced pediatric radiologist (obs1) and a junior radiologist (obs2)...
Article
Full-text available
White matter bundle segmentation using diffusion MRI fiber tractography has become the method of choice to identify white matter fiber pathways in vivo in human brains. However, like other analyses of complex data, there is considerable variability in segmentation protocols and techniques. This can result in different reconstructions of the same in...
Article
Full-text available
Stroke patients vary considerably in terms of outcomes: some patients present 'natural' recovery proportional to their initial impairment (fitters), while others do not (non-fitters). Thus, a key challenge in stroke rehabilitation is to identify individual recovery potential to make personalized decisions for neuro-rehabilitation, obviating the 'on...
Article
Full-text available
In the central nervous system of primates, several pathways are characterized by different spectra of axon diameters. In vivo methods, based on diffusion-weighted magnetic resonance imaging, can provide axon diameter index estimates non-invasively. However, such methods report voxel-wise estimates, which vary from voxel-to-voxel for the same white...
Article
Full-text available
Les récents développements dans le domaine du machine-learning et de la détection automatique d’images ont des répercussions dans de nombreux domaines, y compris dans le domaine de l’agriculture. Cet article présente les travaux de recherches effectués par le Centre de recherche apicole d’Agroscope, l’EPFL, Identitas AG et Apizoom Sàrl, afin de dév...
Article
Full-text available
Cervical cancer remains a major public health concern in developing countries due to financial and human resource constraints. Visual inspection with acetic acid (VIA) of the cervix was widely promoted and routinely used as a low-cost primary screening test in low- and middle-income countries. It can be performed by a variety of health workers and...
Preprint
Full-text available
Multiple sclerosis (MS) is an inflammatory and neurodegenerative disease characterized by diffuse and focal areas of tissue loss. Conventional MRI techniques such as T1-weighted and T2-weighted scans are generally used in the diagnosis and prognosis of the disease. Yet, these methods are limited by the lack of specificity between lesions, their per...
Preprint
Existing reference (RF)-based super-resolution (SR) models try to improve perceptual quality in SR under the assumption of the availability of high-resolution RF images paired with low-resolution (LR) inputs at testing. As the RF images should be similar in terms of content, colors, contrast, etc. to the test image, this hinders the applicability i...
Article
Full-text available
Essential tremor (ET) is the most common movement disorder. Deep brain stimulation is the current gold standard for drug-resistant tremor, followed by radiofrequency lesioning. Stereotactic radiosurgery by Gamma Knife (GK) is considered as a minimally invasive alternative. The majority of procedures aim at the same target, thalamic ventro-intermedi...
Preprint
Full-text available
Despite the successes of deep neural networks on many challenging vision tasks, they often fail to generalize to new test domains that are not distributed identically to the training data. The domain adaptation becomes more challenging for cross-modality medical data with a notable domain shift. Given that specific annotated imaging modalities may...
Preprint
Segmenting histology images into diagnostically relevant regions is imperative to support timely and reliable decisions by pathologists. To this end, computer-aided techniques have been proposed to delineate relevant regions in scanned histology slides. However, the techniques necessitate task-specific large datasets of annotated pixels, which is t...
Preprint
Full-text available
Cancer diagnosis and prognosis for a tissue specimen are heavily influenced by the phenotype and topological distribution of the constituting histological entities. Thus, adequate tissue representation by encoding the histological entities, and quantifying the relationship between the tissue representation and tissue functionality is imperative for...
Preprint
Full-text available
Detecting anomalies in musculoskeletal radiographs is of paramount importance for large-scale screening in the radiology workflow. Supervised deep networks take for granted a large number of annotations by radiologists, which is often prohibitively very time-consuming to acquire. Moreover, supervised systems are tailored to closed set scenarios, e....
Article
Despite the successes of deep neural networks on many challenging vision tasks, they often fail to generalize to new test domains that are not distributed identically to the training data. The domain adaptation becomes more challenging for cross-modality medical data with a notable domain shift. Given that specific annotated imaging modalities may...
Article
Full-text available
Background and Objective Compared to the conventional magnetization-prepared rapid gradient-echo imaging (MPRAGE) MRI sequence, the specialized magnetization prepared 2 rapid acquisition gradient echoes (MP2RAGE) shows a higher brain tissue and lesion contrast in multiple sclerosis (MS) patients. The goal of this work is to retrospectively generate...
Article
Full-text available
Multi-component T2 relaxometry allows probing tissue microstructure by assessing compartment-specific T2 relaxation times and water fractions, including the myelin water fraction. Non-negative least squares (NNLS) with zero-order Tikhonov regularization is the conventional method for estimating smooth T2 distributions. Despite the improved estimati...
Article
Full-text available
White matter bundle segmentation using diffusion MRI fiber tractography has become the method of choice to identify white matter fiber pathways in vivo in human brains. However, like other analyses of complex data, there is considerable variability in segmentation protocols and techniques. This can result in different reconstructions of the same in...
Article
Thanks to its capability of acquiring full-view frames at multiple kilohertz, ultrafast ultrasound imaging unlocked the analysis of rapidly changing physical phenomena in the human body, with pioneering applications such as ultrasensitive flow imaging in the cardiovascular system or shear-wave elastography. The accuracy achievable with these motion...
Article
Full-text available
Significance Axons, the brain’s communication cables, have been described as cylinders since their discovery in 1860. Their structure is linked to how fast they conduct signals and is thus indicative of brain health and function. Here, we demonstrate an interplay between the micromorphology of axons and other extra-axonal structures, showing that a...
Article
Full-text available
Pulmonary hypertension is a hemodynamic disorder defined by an abnormal elevation of pulmonary artery pressure (PAP). Current options for measuring PAP are limited in clinical practice. The aim of this study was to evaluate if electrical impedance tomography (EIT), a radiation-free and non-invasive monitoring technique, can be used for the continuo...
Article
Full-text available
At the typical spatial resolution of MRI in the human brain, approximately 60-90% of voxels contain multiple fiber populations. Quantifying microstructural properties of distinct fiber populations within a voxel is therefore challenging but necessary. While progress has been made for diffusion and T1-relaxation properties, how to resolve intra-voxe...
Article
Full-text available
Recovering the T2 distribution from multi-echo T2 magnetic resonance (MR) signals is challenging but has high potential as it provides biomarkers characterizing the tissue micro-structure, such as the myelin water fraction (MWF). In this work, we propose to combine machine learning and aspects of parametric (fitting from the MRI signal using biophy...
Article
Full-text available
Diffusion MRI (dMRI) represents one of the few methods for mapping brain fiber orientations non-invasively. Unfortunately, dMRI fiber mapping is an indirect method that relies on inference from measured diffusion patterns. Comparing dMRI results with other modalities is a way to improve the interpretation of dMRI data and help advance dMRI technolo...
Preprint
Explainability of deep learning methods is imperative to facilitate their clinical adoption in digital pathology. However, popular deep learning methods and explainability techniques (explainers) based on pixel-wise processing disregard biological entities' notion, thus complicating comprehension by pathologists. In this work, we address this by ad...