AIRE (Automated Invasive Radii Estimation) - tool for estimating the invasive radii of tumor spheroids grown in vitro.

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.
FIRE (FIbeR Extraction) - tool for extracting network architecture from 3d, confocal images of biopolymer networks.

Stein AM et al. An algorithm for extracting the network geometry of three-dimensional collagen gels. J. Microscopy, 232 (3) 463-475, 2008.
       Click image for deformation animation.

BEAMS (Beam Energy And Minimization Simulation) - code for simulating 3d beam network deformation.

Stein AM et al. The micromechanics of collagen-I gels. Complexity, 16, 22-28, 2011.