From individual intensity voxel data to inter-individual probabilistic atlases of biological objects by an interleaved registration-segmentation approach

In this paper we describe an automated processing of plant serial section data for high-resolution 3-D models of internal structures. The processing pipeline includes standardization and registration of large image stacks as well as multiple tissue recognition by a joint registration-segmentation approach. By integrating segmented data from multiple individuals in a common reference, a statistical three-dimensional description is used to represent the inherent biodiversity amongst specimen. Inter-individual 3-D models are a novelty in the context of plant microscopy, and along with meaningful visualisation they deliver new insights into growth and development as well as provide a framework for the integration of functional data.