Publications associées à User-Friendly Image-Based Segmentation and Analysis of Chromosomes

Modular segmentation, spatial analysis and visualization of volume electron microscopy datasets

Volume electron microscopy is the method of choice for the in situ interrogation of cellular ultrastructure at the nanometer scale, and with the increase in large raw image datasets generated, improving computational strategies for image segmentation and s ...

Nature Portfolio2024

Text-to-Microstructure Generation Using Generative Deep Learning

Jamie Paik

Designing novel materials is greatly dependent on understanding the design principles, physical mechanisms, and modeling methods of material microstructures, requiring experienced designers with expertise and several rounds of trial and error. Although rec ...

Wiley-V C H Verlag Gmbh2024

Self-supervised Dense Representation Learning for Live-Cell Microscopy with Time Arrow Prediction

Max Stieber, Martin Weigert, Benjamin Tobias Gallusser

State-of-the-art object detection and segmentation methods for microscopy images rely on supervised machine learning, which requires laborious manual annotation of training data. Here we present a self-supervised method based on time arrow prediction pre-t ...

Springer International Publishing Ag2023

Automated neuron tracking inside moving and deforming C. elegans using deep learning and targeted augmentation

Sahand Jamal Rahi, Kseniia Korchagina

Reading out neuronal activity from three-dimensional (3D) functional imaging requires segmenting and tracking individual neurons. This is challenging in behaving animals if the brain moves and deforms. The traditional approach is to train a convolutional n ...

Nature Portfolio2023

lifex-ep: a robust and efficient software for cardiac electrophysiology simulations

Alfio Quarteroni, Francesco Regazzoni, Marco Fedele, Stefano Pagani

Background: Simulating the cardiac function requires the numerical solution of multi-physics and multi-scale mathematical models. This underscores the need for streamlined, accurate, and high-performance computational tools. Despite the dedicated endeavors ...

BMC2023

impresso Text Reuse at Scale. An interface for the exploration of text reuse data in semantically enriched historical newspapers

Maud Ehrmann, Matteo Romanello

Text Reuse reveals meaningful reiterations of text in large corpora. Humanities researchers use text reuse to study, e.g., the posterior reception of influential texts or to reveal evolving publication practices of historical media. This research is often ...

2023

Latency Interfaces for Systems Code

Rishabh Ramesh Iyer

This thesis demonstrates that it is feasible for systems code to expose a latency interface that describes its latency and related side effects for all inputs, just like the code's semantic interface describes its functionality and related side effects. S ...

EPFL2023

BMAT: An open-source BIDS managing and analysis tool

Meritxell Bach Cuadra, Benoît Macq, Francesco La Rosa, Maxence Charles F Wynen

Magnetic Resonance Imaging (MRI) is an established technique to study in vivo neurological disorders such as Multiple Sclerosis (MS). To avoid errors on MRI data organization and automated processing, a standard called Brain Imaging Data Structure (BIDS) h ...

ELSEVIER SCI LTD2022

Simple automation of SEM-EDS spectral maps analysis with Python and the edxia framework

Karen Scrivener, Fabien Jacques Michel Georget, William Wilson

In a recent article, we described the edxia framework, a user-friendly framework to analyse the microstructure of cementitious materials using SEM-EDS hypermaps. The manual approach presented was shown to be efficient to answer the relevant scientific ques ...

WILEY2022

Dynamic Personalized Ranking

Jérémie Rappaz

Personalized ranking methods are at the core of many systems that learn to produce recommendations from user feedbacks. Their primary objective is to identify relevant items from very large vocabularies and to assist users in discovering new content. These ...

EPFL2022

Deep learning-based analysis of multiple sclerosis lesions with high and ultra-high field MRI

Francesco La Rosa

Multiple sclerosis (MS) is the most common demyelinating disease of the central nervous system and affects almost 3 million people worldwide. There is currently no cure for MS, and its symptoms, starting with fatigue and weakness, often progress over time ...

EPFL2022

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

Development of the RAPTOR suite of codes towards real-time reconstruction of JET discharges

Federico Alberto Alfredo Felici

The RAPTOR suite of codes combines real-time model-based predictions of the plasma state with the available diagnostic measurements. Following the work on TCV and ASDEX-Upgrade, this paper presents the implementation of the RAPTOR suite for JET. This suite ...

2021

Multi-Step Critiquing User Interface for Recommender Systems

Boi Faltings, Diego Matteo Antognini, Diana Andreea Petrescu

Recommendations with personalized explanations have been shown to increase user trust and perceived quality and help users make better decisions. Moreover, such explanations allow users to provide feedback by critiquing them. Several algorithms for recomme ...

ASSOC COMPUTING MACHINERY2021

Computational tool for stock-constrained design of structures

Corentin Jean Dominique Fivet, Jan Friedrich Georg Brütting, Jonas Warmuth

Designing structures from reused elements is becoming an increasingly important design task for structural engineers as it has potential to significantly reduce adverse environmental impacts of building structures. To allow for a broad application of this ...

2021

HISTOBREAST, a collection of brightfield microscopy images of Haematoxylin and Eosin stained breast tissue

Tiberiu Totu

Modern histopathology workflows rely on the digitization of histology slides. The quality of the resulting digital representations, in the form of histology slide image mosaics, depends on various specific acquisition conditions and on the image processing ...

2020

Synchrotron-based phase-contrast micro-CT as a tool for understanding pulmonary vascular pathobiology and the 3-D microanatomy of alveolar capillary dysplasia

Goran Lovric

This study aimed to explore the value of synchrotron-based phase-contrast microcomputed tomography (micro-CT) in pulmonary vascular pathobiology. The microanatomy of the lung is complex with intricate branching patterns. Tissue sections are therefore diffi ...

AMER PHYSIOLOGICAL SOC2020

Meteolakes: An operational online three-dimensional forecasting platform for lake hydrodynamics

Alfred Johny Wüest, Damien Bouffard, Theo Baracchini

Environmental management depends on high-quality monitoring and its meaningful interpretation. The combination of local weather dynamics, regional anthropogenic stresses and global environmental changes make the evaluation of monitoring information in dyna ...

PERGAMON-ELSEVIER SCIENCE LTD2020

Human-friendly solutions for last-centimeter drone delivery

Przemyslaw Mariusz Kornatowski

The popularity of delivery drones is constantly increasing due to their ability to deliver packages more rapidly and economically than current transportation methods. Consequently, drones have been employed by logistics companies for delivering payloads to ...

EPFL2020

Texture-driven parametric snakes for semi-automatic image segmentation

Michaël Unser, Adrien Raphaël Depeursinge, Anaïs Laure Marie-Thérèse Badoual

We present a texture-driven parametric snake for semi-automatic segmentation of a single and closed structure in an image. We propose a new energy functional that combines intensity and texture information. The two types of image information are balanced u ...

ACADEMIC PRESS INC ELSEVIER SCIENCE2019