Related papers: A Semi-automatic Cell Tracking Process Towards Com…
Motif discovery is a powerful and insightful method to quantify network structures and explore their function. As a case study, we present a comprehensive analysis of regulatory motifs in the connectome of the model organism Caenorhabditis…
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…
The ability to acquire large-scale recordings of neuronal activity in awake and unrestrained animals poses a major challenge for studying neural coding of animal behavior. We present a new instrument capable of recording intracellular…
To accelerate the development of strategies for cartilage tissue engineering, models are necessary to study the interactions between cellular dynamics and scaffold (SC) porosity. In experiments, cells are seeded in a porous SC where over a…
Understanding principles of neurolocomotion requires the synthesis of neural activity, sensory feedback, and biomechanics. The nematode \textit{C. elegans} is an ideal model organism for studying locomotion in an integrated neuromechanical…
We introduce a generic, purely mechanical model for environment sensitive motion of mammalian cells that is applicable to chemotaxis, haptotaxis, and durotaxis as modes of motility. It is able to theoretically explain all relevant…
The phase field model can accurately simulate the evolution of microstructures with complex morphologies, and it has been widely used for cell modeling in the last two decades. However, compared to other cellular models such as the…
How microorganisms respond to and interact with their environment can vary significantly from individual to individual, which can have important microbiological and ecological implications. However, most microscopy techniques can only…
Live-cell microscopy allows to go beyond measuring average features of cellular populations to observe, quantify and explain biological heterogeneity. Deep Learning-based instance segmentation and cell tracking form the gold standard…
We propose a general framework for a collaborative machine learning system to assist bioscience researchers with the task of labeling specific cell identities from microscopic still or video imaging. The distinguishing features of this…
Single-cell trajectory analysis aims to reconstruct the biological developmental processes of cells as they evolve over time, leveraging temporal correlations in gene expression. During cellular development, gene expression patterns…
Epigenetic Tracking (ET) is an Artificial Embryology system which allows for the evolution and development of large complex structures built from artificial cells. In terms of the number of cells, the complexity of the bodies generated with…
Caenorhabditis elegans (C. elegans) is an excellent model organism because of its short lifespan and high degree of homology with human genes, and it has been widely used in a variety of human health and disease models. However, the…
Background Despite its status as a model organism, the development of Caenorhabditis elegans is not necessarily archetypical for nematodes. The phylum Nematoda is divided into the Chromadorea (indcludes C. elegans) and the Enoplea. Compared…
Control is essential to the functioning of any neural system. Indeed, under healthy conditions the brain must be able to continuously maintain a tight functional control between the system's inputs and outputs. One may therefore hypothesise…
Animal behaviors are sometimes decomposable into discrete, stereotyped elements. In one model, such behaviors are triggered by specific commands; in the extreme case, the discreteness of behavior is traced to the discreteness of action…
Amoeboid motion is a dynamic mode of cell motility essential for processes such as the immune response and wound healing. This review examines recent developments in the mathematical and computational modeling of amoeboid crawling, focusing…
The 1mm roundworm C. elegans is a model organism used in many sub-areas of biology to investigate different types of biological processes. In order to complement the n-vivo analysis with computer-based investigations, several methods have…
We describe a straightforward, automated line tracking method to visualize within optical resolution the contour of linear macromolecules as they rearrange shape as a function of time by Brownian diffusion and under external fields such as…
The dynamics of complex systems generally include high-dimensional, non-stationary and non-linear behavior, all of which pose fundamental challenges to quantitative understanding. To address these difficulties we detail a new approach based…