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To maintain homeostasis, living cells process information with networks of interacting molecules. Traditional models for cellular information processing have focused on networks of chemical reactions between molecules. Here, we describe how…
The automated analysis of microscopy images is a challenge in the context of single-cell tracking and quantification. This work has as goals the study of the performance of deep learning for segmenting microscopy images and the improvement…
Ascertaining the collective viability of cells in different cell culture conditions has typically relied on averaging colorimetric indicators and is often reported out in simple binary readouts. Recent research has combined viability…
Conventional cell tracking methods detect multiple cells in each frame (detection) and then associate the detection results in successive time-frames (association). Most cell tracking methods perform the association task independently from…
This paper presents a new method for automatic quantification of ellipse-like cells in images, an important and challenging problem that has been studied by the computer vision community. The proposed method can be described by two main…
The study of biological systems witnessed a pervasive cross-fertilization between experimental investigation and computational methods. This gave rise to the development of new methodologies, able to tackle the complexity of biological…
This work presents a comprehensive performance analysis and optimization of a multiscale agent-based cellular simulation. The optimizations applied are guided by detailed performance analysis and include memory management, load balance, and…
Simulations of biophysical systems inevitably include steps that correspond to time integrations of ordinary differential equations. These equations are often related to enzyme action in the synthesis and destruction of molecular species,…
This chapter provides a brief introduction to the theory and practice of spatial stochastic simulations. It begins with an overview of different methods available for biochemical simulations highlighting their strengths and limitations.…
Image processing applications are common in every field of our daily life. However, most of them are very complex and contain several tasks with different complexities which result in varying requirements for computing architectures.…
Live cell culture is crucial in biomedical studies for analyzing cell properties and dynamics in vitro. This study focuses on segmenting unstained live cells imaged with bright-field microscopy. While many segmentation approaches exist for…
Bioelectrochemistry is crucial for understanding biological functions and driving applications in synthetic biology, healthcare, and catalysis. However, current simulation methods fail to capture both the stochastic nature of molecular…
Improving the energy efficiency of mobile applications is a topic that has gained a lot of attention recently. It has been addressed in a number of ways such as identifying energy bugs and developing a catalog of energy patterns. Previous…
Sequential sampling models (SSMs) are a widely used framework describing decision-making as a stochastic, dynamic process of evidence accumulation. SSMs popularity across cognitive science has driven the development of various software…
We present Bionic Tracking, a novel method for solving biological cell tracking problems with eye tracking in virtual reality using commodity hardware. Using gaze data, and especially smooth pursuit eye movements, we are able to track cells…
In non-linear systems, where explicit analytic solutions usually can't be found, visualisation is a powerful approach which can give insights into the dynamical behaviour of models; it is also crucial for teaching this area of mathematics.…
Medical image computing software is essential for identifying imaging biomarkers that can support diagnosis, prognosis, treatment planning, and clinical research. However, the lack of standardized, user-friendly, and reproducible software…
Optical metasurfaces composed of precisely engineered nanostructures have gained significant attention for their ability to manipulate light and implement distinct functionalities based on the properties of the incident field. Computational…
Drawing and visualisation of molecular structures are some of the most common tasks carried out in structural glycobiology, typically using various software. In this perspective article, we outline developments in the computational tools…
Cell tracking is an essential tool in live-cell imaging to determine single-cell features, such as division patterns or elongation rates. Unlike in common multiple object tracking, in microbial live-cell experiments cells are growing,…