Fast Interactive Integration of Cross- Sectional Image Datasets and Surface Data for Morphometric Analysis Oscar MERUVIA-PASTOR 1a , Jung SOH a , Mei XIAO a , Eric SCHMIDT b , Cairine LOGAN b , Julia C. BOUGHNER b , Nicholas JONES b , David OSBORN a , Johanna SANTIAGO a , Julian GITTLEMAN b , Benedikt HALLGRÍMSSON b , Christoph W. SENSEN a a Sun Center of Excellence for Visual Genomics, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Calgary b Morphometrics Laboratory, Department of Cell Biology & Anatomy Faculty of Medicine, University of Calgary Abstract. To investigate external facial morphology and cell proliferation patterns and their relationship with cleft lip malformation in mice, we need to compare samples of mice tissue photographs and surface reconstructions from micro-CT scans obtained from mouse embryos. Tissue samples obtained through digital photography are typically misaligned with respect to each other, which prevents further analysis. We have developed a system for fast interactive alignment of these image stacks for volume reconstruction and data visualization and analysis in 3D. The system is designed to work in multiprocessor environments and can utilize an arbitrary number of processors, cutting down significantly the turnaround time and allowing users to quickly process sets of hundreds of high resolution images using a combination of automated and interactive tools. Additional modules are used to reconstruct the shape of the original subject. Our system is interactive, fully scalable and can be applied to any photographic sliced dataset, regardless of subject and reduces significantly the processing time for stack alignment. Keywords. Image Registration, Histology, Parallel Processing, 3D Surface Reconstruction, Mouse Development 1. Background Identifying cell proliferation changes within and across subjects at different stages of growth is important in morphometrics research. In particular, we want to model the relationship between cell proliferation patterns, external facial morphology and cleft lip malformation in mice. To investigate this relationship, various types of data sets are generated for each mouse embryo specimen. A 3D representation of the surface of a subject is obtained by processing MRI, CT or micro-CT scans (see Figure 1). 1 Corresponding Author: Dr. Oscar Meruvia-Pastor (oscar.dot.meruvia@ucalgary.dot.ca)