Nature Inspired Phenotype Analysis with 3D Model Representation Optimization

Part of the Advances in Intelligent Systems and Computing book series (AISC, volume 237)


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.

The optimized 3D models are used in the analysis of phenotypical differences originating from experimental conditions by extracting related shape features from the model. We use two different sets of 3D models. We investigate the lactiferous duct of newborn mice to gain understanding of environmental directed branching. We consider that the lactiferous duct has an innate blue-print of its arborazation and assume this blue-print is kind of encoded in an innate L-system. We analyze the duct as it is exposed to different environmental conditions and reflect on the effect on the innate L-system. In order to make sure we can extract the branch structure in the right manner we analyze 3D models of the zebrafish embryo; these are simpler compared to the lactiferous duct and will ensure us that measuring features can result in the separation of different treatments on the basis of differences in the phenotype.

Our system can deal with the complex 3D models, the features separate the experimental conditions. The results provide a means to reflect on the manipulation of an L-system through external factors.


biological model 3D reconstruction phenotype measurement L-System 


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Copyright information

© Springer International Publishing Switzerland 2014

Authors and Affiliations

  1. 1.Section Imaging & BioInformatics, Leiden Institute of Advanced Computer ScienceLeiden UniversityLeidenThe Netherlands

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