Image analysis and microscopy:
Mechanistic modeling of complex biological processes provides a means to understand dynamic regulation in a number of different contexts. However, most models are limited in their ability to make testable predictions accesible to biologists since they simplify the geometry, boundary conditions, initial conditions, and other spatio-temporal information. To incorporate geometric data into the models, we developed a methodology to reconstruct 3D meshes from confocal z-sections of the specimen. The prepatterns that specify the initial and boundary conditions are obtained by scanning-laser confocal microscopy of fluorescently labeled proteins and mRNAs. The distributions are incorporated directly into the 3D models, the governing equations are solved, and the output distributions are compared with the average embryo images.