Matlab Tools for Tumor Spheroid and Collagen Network Analysis
MATLAB tools from the PhD thesis and postdoc, before 2011
Three MATLAB tools written during the PhD and postdoc: AIRE for tumour spheroid invasive radii, FIRE for extracting network geometry from confocal images, and BEAMS for simulating beam network deformation.
These are MATLAB tools written during my PhD thesis and postdoctoral research, before 2011. They are kept here for the record and for anyone who finds them through the papers below.
- AIRE — Automated Invasive Radii Estimation: tool for estimating the invasive radii of tumor spheroids grown in vitro.
- FIRE — FIbeR Extraction: tool for extracting network architecture from 3d, confocal images of biopolymer networks.
- BEAMS — Beam Energy And Minimization Simulation: code for simulating 3d beam network deformation.
Papers
Stein AM et al. Estimating the cell density and invasive radius of 3d glioblastoma tumor spheroids grown in vitro. Applied Optics, 46(22):5110–5118, 2007.
Stein AM et al. An algorithm for extracting the network geometry of three-dimensional collagen gels. J. Microscopy, 232(3) 463–475, 2008.
Stein AM et al. The micromechanics of collagen-I gels. Complexity, 16, 22–28, 2011.