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Related Experiment Video

Updated: Jul 12, 2025

Biomechanical Testing of Murine Tendons

Biomechanical Testing of Murine Tendons

Published on: October 15, 2019

General, open-source vertex modeling in biological applications using Tissue Forge.

T J Sego¹, Tien Comlekoglu^2,3, Shayn M Peirce²

¹Department of Medicine, University of Florida, Gainesville, FL, USA. timothy.sego@ufl.edu.

Scientific Reports

|October 19, 2023

Summary

This summary is machine-generated.

We developed an open-source vertex model methodology in Tissue Forge, enhancing accessibility and reproducibility for studying multicellular systems. This physics-based approach integrates with particle-based methods for complex biological simulations.

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Last Updated: Jul 12, 2025

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A Method for 3D Reconstruction and Virtual Reality Analysis of Glial and Neuronal Cells

A Method for 3D Reconstruction and Virtual Reality Analysis of Glial and Neuronal Cells

Published on: September 28, 2019

Area of Science:

Multicellular systems biology
Biophysics
Computational biology

Background:

Vertex models are crucial for understanding epithelial tissue dynamics, including cell rearrangement and tissue folding.
Existing vertex models are often closed-source, limiting reproducibility and accessibility for researchers.
A need exists for open-source, extensible vertex modeling tools compatible with diverse computational approaches.

Purpose of the Study:

To develop a physics-based vertex model methodology within an open-source framework.
To enhance the accessibility and reproducibility of vertex modeling for multicellular systems research.
To enable the creation of mixed-method models by integrating vertex and particle-based formalisms.

Main Methods:

Implemented a physics-based vertex model methodology in Tissue Forge, an open-source particle-based simulation environment.
Described vertex model properties and processes based on vertices for seamless integration.
Leveraged Tissue Forge features for interactive simulation, real-time visualization, and multi-language support (C, C++, Python).

Main Results:

Successfully created an open-source, extensible vertex modeling methodology.
Demonstrated the methodology with a vertex model of cell sorting.
Showcased a mixed-method model combining vertex- and particle-based approaches for cell migration.

Conclusions:

The developed methodology provides accessible and reproducible vertex modeling for various scientific disciplines.
Integration with Tissue Forge facilitates the development of complex, mixed-method models of multicellular systems.
The open-source nature encourages community contributions and further advancements in the field.