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SOAX: a software for quantification of 3D biopolymer networks
Ting Xu1, Dimitrios Vavylonis2, Feng-Ching Tsai3
1Department of Computer Science and Engineering, Lehigh University, Bethlehem, Pennsylvania, USA.
Scientific Reports
|March 14, 2015
Summary
SOAX software accurately extracts 3D biopolymer network centerlines and junctions. This open-source tool aids quantitative analysis of filamentous networks in cell biology and biophysics.
Area of Science:
- Cell Biology
- Biophysics
- Bioimage Analysis
Background:
- Filamentous biopolymer networks are crucial in cells and tissues.
- Confocal microscopy images these networks.
- Quantitative analysis of 3D network geometry and topology is limited by software availability.
Purpose of the Study:
- Develop a software tool to quantify 3D biopolymer networks.
- Enable accurate extraction of network centerlines and junction localization.
- Provide a user-friendly platform for analysis.
Main Methods:
- Developed SOAX (Stretching Open Active Contours) software.
- Utilized SOACs for centerline extraction and junction identification.
- Implemented a performance quantification method for parameter optimization.
Main Results:
- SOAX accurately extracts centerlines and identifies junctions in 3D biopolymer networks.
- The software offers open-source, user-friendly 2D/3D visualization and manual editing.
- Demonstrated SOAX's potential across diverse biopolymer network types.
Conclusions:
- SOAX addresses the scarcity of tools for quantitative 3D network analysis.
- The software facilitates deeper insights into cell biology and biophysics.
- SOAX enables precise, quantitative study of filamentous networks.
