A modeling algorithm for exploring the architecture and construction of bird nests

Natural biological structures are often complex and cannot be mapped directly to genes, being therefore impossible to explore by traditional biological tools. In contrast, digitizing these structures enables to explore their properties and behavior under specific conditions, by means of computational manipulations, simulations, and analyses. We describe a generic algorithm for the digitization and exploration of the complex structures exhibited by common, interwoven bird nests. This algorithm takes as input computerized tomographic scans of the studied Dead-Sea Sparrow (Passer moabiticus) nest, identifies and isolates each branch entity within the three-dimensional data and finally extracts the characteristics of each branch. The result is a reliable three-dimensional numerical model of the nest that contains a complete geometric dataset per each of its components, e.g. dimensions and contact points with neighboring components, as well as global properties, e.g. density distribution and network structure. Based on these, we were able to simulate various models of the nest construction process. Altogether, the described algorithm and possible derivatives thereof could be a valuable tool in studying the structure-function relationships of similarly complex biological objects.