A semi-automatic method to extract canal pathways in 3D micro-CT images of Octocorals.

The long-term goal of our study is to understand the internal organization of the octocoral stem canals, as well as their physiological and functional role in the growth of the colonies, and finally to assess the influence of climatic changes on this species. Here we focus on imaging tools, namely acquisition and processing of three-dimensional high-resolution images, with emphasis on automated extraction of canal pathways. Our aim was to evaluate the feasibility of the whole process, to point out and solve - if possible - technical problems related to the specimen conditioning, to determine the best acquisition parameters and to develop necessary image-processing algorithms.