**1. Introduction**

Advanced biomechanical models of biological tissues should be based on statistical morphometry of tissue architecture. A quantitative description of the microscopic properties of real tissue samples is an advantage when devising computer models that are statistically similar to biological tissues in physiological or pathological conditions. The recent development of X-ray microtomography (micro-CT) has introduced resolution similar to that of routine histology. The aim of this chapter is to review and discuss both automatic image processing and interactive, unbiased stereological tools available for micro-CT scans and histological micrographs. We will demonstrate the practical usability of micro-CT in two different types of three-dimensional (3-D) *ex vivo* samples: (i) bone scaffolds used in tissue engineering and (ii) microvascular corrosion casts.
