Nature Inspired Phenotype Analysis with 3D Model Representation Optimization

In biology 3D models are made to correspond with true nature so as to use these models for a precise analysis. The visualization of these models helps in the further understanding and conveying of the research questions. Here we use 3D models in gaining understanding on branched structures. To that end we will make use of L-systems and will attempt to use the results of our analysis for the gaining of understanding of these L-systems. To perform our analysis we will have to optimize the 3D models. There are lots of different methods to produce such 3D model. For the study of micro-anatomy, however, the possibilities are limited. In planar sampling, the resolution in the sampling plane is higher than the planes perpendicular to the sampling plane. Consequently, 3D models are under sampled along, at least, one axis. In this paper we present a pipeline for reconstruction of a stack of images. We devised a method to convert the under sampled stack of contours into a uniformly distributed point cloud. The point cloud as a whole is integrated in construction of a surface that accurately represents the shape. In the pipeline the 3D dataset is processed and its quality gradually upgraded so that accurate features can be extracted from under sampled dataset.