A concise review of optical, physical and isotropic fractionator techniques in neuroscience studies, including recent developments.

Stereology is a collection of methods which makes it possible to produce interpretations about actual three-dimensional features of objects based on data obtained from their two-dimensional sections or images. Quantitative morphological studies of the central nervous system have undergone significant development. In particular, new approaches known as design-based methods have been successfully applied to neuromorphological research. The morphology of macroscopic and microscopic structures, numbers of cells in organs and structures, and geometrical features such as length, volume, surface area and volume components of the organ concerned can be estimated in an unbiased manner using stereological techniques. The most practical and simplest stereological method is the fractionator technique, one of the most widely used methods for total particle number estimation. This review summarizes fractionator methods in theory and in practice. The most important feature of the methods is the simplicity of its application and underlying reasoning. Although there are three different types of the fractionator method, physical, optical and isotropic (biochemical), the logic underlying its applications remains the same. The fractionator method is one of the strongest and best options among available methods for estimation of the total number of cells in a given structure or organ. The second part of this review focuses on recent developments in stereology, including how to deal with lost caps, with tissue section deformation and shrinkage, and discusses issues of calibration, particle identification, and the role of stereology in the era of a non-histological alternative to counting of cells, the isotropic fractionator (brain soup technique).