Dataset Information

Modelling cell surface dynamics and cell-cell interactions using Cell Studio: a three-dimensional visualization tool based on gaming technology.

ABSTRACT: Predictive modelling of complex biological systems and biophysical interactions requires the inclusion of multiple nano- and micro-scale events. In many scenarios, however, numerical solutions alone do not necessarily enhance the understanding of the system. Instead, this work explores the use of an agent-based model with visualization capabilities to elucidate interactions between single cells. We present a model of juxtacrine signalling, using Cell Studio, an agent-based modelling system, based on gaming and three-dimensional visualization tools. The main advantages of the system are its ability to apply any cell geometry and to dynamically visualize the diffusion and interactions of the molecules within the cells in real time. These provide an excellent tool for obtaining insight about different biological scenarios, as the user may view the dynamics of a system and observe its emergent behaviour as it unfolds. The agent-based model was validated against the results of a mean-field model of Notch receptors and ligands in two neighbouring cells. The conversion to an agent-based model is described in detail. To demonstrate the advantages of the model, we further created a filopodium-mediated signalling model. Our model revealed that diffusion and endocytosis alone are insufficient to produce significant signalling in a filopodia scenario. This is due to the bottleneck at the cell-filopodium contact region and the long distance to the end of the filopodium. However, allowing active transport of ligands into filopodia enhances the signalling significantly compared with a face-to-face scenario. We conclude that the agent-based approach can provide insights into mechanisms underlying cell signalling. The open-source model can be found in the Internet hosting service GitHub.

SUBMITTER: Liberman A

PROVIDER: S-EPMC6893490 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature

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Modelling cell surface dynamics and cell-cell interactions using Cell Studio: a three-dimensional visualization tool based on gaming technology.

Liberman Asaf A Mussel Matan M Kario Danny D Sprinzak David D Nevo Uri U

Journal of the Royal Society, Interface 20191127 160

Predictive modelling of complex biological systems and biophysical interactions requires the inclusion of multiple nano- and micro-scale events. In many scenarios, however, numerical solutions alone do not necessarily enhance the understanding of the system. Instead, this work explores the use of an agent-based model with visualization capabilities to elucidate interactions between single cells. We present a model of juxtacrine signalling, using Cell Studio, an agent-based modelling system, base ...[more]

PMID: 31771451

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Project description:Photoacoustic (PA) imaging (or optoacoustic imaging) is a novel biomedical imaging method in biological and medical research. This modality performs morphological, functional, and molecular imaging with and without labels in both microscopic and deep tissue imaging domains. A variety of innovations have enhanced 3D PA imaging performance and thus has opened new opportunities in preclinical and clinical imaging. However, the 3D visualization tools for PA images remains a challenge. There are several commercially available software packages to visualize the generated 3D PA images. They are generally expensive, and their features are not optimized for 3D visualization of PA images. Here, we demonstrate a specialized 3D visualization software package, namely 3D Photoacoustic Visualization Studio (3D PHOVIS), specifically targeting photoacoustic data, image, and visualization processes. To support the research environment for visualization and fast processing, we incorporated 3D PHOVIS onto the MATLAB with graphical user interface and developed multi-core graphics processing unit modules for fast processing. The 3D PHOVIS includes following modules: (1) a mosaic volume generator, (2) a scan converter for optical scanning photoacoustic microscopy, (3) a skin profile estimator and depth encoder, (4) a multiplanar viewer with a navigation map, and (5) a volume renderer with a movie maker. This paper discusses the algorithms present in the software package and demonstrates their functions. In addition, the applicability of this software to ultrasound imaging and optical coherence tomography is also investigated. User manuals and application files for 3D PHOVIS are available for free on the website (www.boa-lab.com). Core functions of 3D PHOVIS are developed as a result of a summer class at POSTECH, "High-Performance Algorithm in CPU/GPU/DSP, and Computer Architecture." We believe our 3D PHOVIS provides a unique tool to PA imaging researchers, expedites its growth, and attracts broad interests in a wide range of studies.

Project description:BackgroundThree-dimensional Surface Imaging (3DSI) is a well-established method to objectively monitor morphological changes in the female breast in the field of plastic surgery. In contrast, in radiation oncology we are still missing effective tools, which can objectively and reproducibly assess and document adverse events in breast cancer radiotherapy within the framework of clinical studies. The aim of the present study was to apply structured-light technology as a non-invasive and objective approach for the documentation of cosmetic outcome and early effects of breast radiotherapy as a proof of principle.MethodsWeekly 3DSI images of patients receiving either conventionally fractionated radiation treatment (CF-RT) or hypofractionated radiation treatment (HF-RT) were acquired during the radiotherapy treatment and clinical follow-up. The portable Artec Eva scanner (Artec 3D Inc., Luxembourg) recorded 3D surface images for the analysis of breast volumes and changes in skin appearance. Statistical analysis compared the impact of the two different fractionation regimens and the differences between the treated and the contralateral healthy breast.ResultsOverall, 38 patients and a total of 214 breast imaging sessions were analysed. Patients receiving CF-RT showed a significantly higher frequency of breast erythema compared to HF-RT (93.3% versus 34.8%, p = 0.003) during all observed imaging sessions. Moreover, we found a statistically significant (p < 0.05) volumetric increase of the treated breast of the entire cohort between baseline (379 ± 196 mL) and follow-up imaging at 3 months (437 ± 224 mL), as well as from week 3 of radiotherapy (391 ± 198 mL) to follow-up imaging. In both subgroups of patients undergoing either CF-RT or HF-RT, there was a statistically significant increase (p < 0.05) in breast volumes between baseline and 3 months follow-up. There were no statistically significant skin or volumetric changes of the untreated healthy breasts.ConclusionsThis is the first study utilizing 3D structured-light technology as a non-invasive and objective approach for the documentation of patients receiving breast radiotherapy. 3DSI offers potential as a non-invasive tool to objectively and precisely monitor the female breast in a radiooncological setting, allowing clinicians to objectively distinguish outcomes of different therapy modalities.

Dataset Information

Modelling cell surface dynamics and cell-cell interactions using Cell Studio: a three-dimensional visualization tool based on gaming technology.

Publications

Modelling cell surface dynamics and cell-cell interactions using Cell Studio: a three-dimensional visualization tool based on gaming technology.

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