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101 Publications visible to you, out of a total of 101
A Generalizable Approach for Network Flow Image Representation for Deep Learning

Abstract

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Authors: Stefan Machmeier, Manuel Trageser, Marcus Buchwald, Vincent Heuveline

Date Published: 16th Oct 2023

Publication Type: Journal

Finite element approximation of dielectrophoretic force driven flow problems

Abstract (Expand)

In this paper, we propose a full discretization scheme for the instationary thermal-electro-hydrodynamic (TEHD) Boussinesq equations. These equations model the dynamics of a non-isothermal, dielectric …f a non-isothermal, dielectric fluid under the influence of a dielectrophoretic (DEP) force. Our scheme combines an H 1 -conformal finite element method for spatial discretization with a backward differentiation formula (BDF) for time stepping. The resulting scheme allows for a decoupled solution of the individual parts of this multi-physics system. Moreover, we derive a priori convergence rates that are of first and second order in time, depending on how the individual ingredients of the BDF scheme are chosen and of optimal order in space. In doing so, special care is taken of modeling the DEP force, since its original form is a cubic term. The obtained error estimates are verified by numerical experiments.

Authors: Philipp Gerstner, Vincent Heuveline

Date Published: 1st May 2023

Publication Type: Journal

Multi-view-AE: A Python package for multi-view autoencoder models

Abstract

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Authors: Ana Lawry Aguila, Alejandra Jayme, Nina Montaña-Brown, Vincent Heuveline, Andre Altmann

Date Published: 1st May 2023

Publication Type: Journal

Implementation Techniques for SPMD Kernels on CPUs

Abstract

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Authors: Joachim Meyer, Aksel Alpay, Sebastian Hack, Holger Fröning, Vincent Heuveline

Date Published: 18th Apr 2023

Publication Type: Journal

One Pass to Bind Them: The First Single-Pass SYCL Compiler with Unified Code Representation Across Backends

Abstract

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Authors: Aksel Alpay, Vincent Heuveline

Date Published: 18th Apr 2023

Publication Type: Journal

ACSEG: AUTOMATED 3D CYTOPLASM SEGMENTATION IN SOFT X-RAY TOMOGRAPHY

Abstract (Expand)

The structure of cells is a key to understanding cellular function, diagnosis of pathological conditions, and development of new treatments. Soft X-ray tomography (SXT) is a unique tool to image cellular … structure without fixation or labeling at high spatial resolution and throughput. Ongoing improvements in faster acquisition times increase demand for accelerated image analysis. Currently, the automatic segmentation of cellular structures is a major bottleneck in the SXT data analysis pipeline. In this paper, we introduce an automated 3D cytoplasm segmentation model - ACSeg - by use of semi-automatically segmented labels and 3D U-Net, implemented in the online platform Biomedisa. The segmentation model is trained on semi-automatically labeled datasets and shows rapid convergence to high-accuracy segmentation, therefore reducing time and labor. ACSeg trained on 43 SXT tomograms of human immune T cells, the model successfully segmented unseen SXT tomograms of human hepatocyte-derived carcinoma cells, mouse microglia, and embryonic fibroblast cells. Furthermore, we could diversify the model by adding only 6 specific SXT tomograms, showing the potential for the development of an optimal experimental design. The ACSeg is published on the open image segmentation platform Biomedisa, enabling high-throughput analysis of cell volume and structure of cytoplasm in diverse cell types. The approach can be expanded for automatic segmentation of other organelles visualized by SXT, providing means for structural analysis of cell remodeling under different pathogens at statistically significant sizes, therefore enabling the development of novel drug treatments.

Authors: Ayse Erozan, Philipp Lösel, Vincent Heuveline, Venera Weinhardt

Date Published: 5th Apr 2023

Publication Type: Journal

A “two-in-one hit” model of shortcut carcinogenesis in MLH1 Lynch syndrome carriers

Abstract

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Authors: Aysel Ahadova, Albrecht Stenzinger, Toni Seppälä, Robert Hüneburg, Matthias Kloor, Hendrik Bläker, Jan-Niklas Wittemann, Volker Endris, Leonie Gerling, Veit Bertram, Marie Theres Neumuth, Johannes Witt, Sebastian Graf, Glen Kristiansen, Oliver Hommerding, Saskia Haupt, Alexander Zeilmann, Vincent Heuveline, Daniel Kazdal, Johannes Gebert, Magnus von Knebel Doeberitz, Jukka-Pekka Mecklin, Jacob Nattermann

Date Published: 11th Mar 2023

Publication Type: Journal

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