The Stereology and 3D Volume Analyses in Nervous Tissue

This chapter provides a crash course for those interested in how an object of interest or signal in the nervous system can be quantified and the volume or features of a brain region can be analyzed with systematic computation. This chapter does not attempt to provide theoretical derivation, nor exhaust all infrequently used methods. Instead, practical uses and caveats are provided followed by the actual practice of the quantitation of commonly encountered signals or objects of interest in neuroscience using a brain sample as an example. This chapter first focuses on quantification of objects in nervous tissues in which the vast number of signals can be estimated free of systematic or methodological bias through sampling in a 3-dimensional (3D) volume using stereology in Sections 2–6. Whereas, computational analysis of the 3D volume and shape features of a region of interest (ROI) in the brain are demonstrated in Section 7.