Biology Reference
In-Depth Information
Chapter 3
The Stereology and 3D Volume Analyses in Nervous Tissue
Rabindra P. Singh , Li Shen , and Feng C. Zhou
Abstract
This chapter provides a crash course for those interested in how an object of interest or signal in the nervous
system can be quantifi ed 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 quan-
titation of commonly encountered signals or objects of interest in neuroscience using a brain sample as an
example. This chapter fi rst focuses on quantifi cation 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.
Key words:
Stereology, 3-Dimensional cell counting, Optical fractionator, Segmentation, Registration,
Voxel-based morphometry, Surface-based morphometry
1. Introduction
Stereology provides an unbiased method for estimating the number
of objects of interests (OI), such as cells, axon terminals or vesicular
terminals, dendritic spines, or other distinct cellular structures
identifi ed by Nissl staining, antibodies, hybridized mRNA, and
so forth, in addition to estimating morphological attributes, such
as length, volume, surface area, or other attributes of interest.
Stereology involves systematic random sampling. For estimating
populations of discrete objects, length or cell volumes, the more
effi cient protocols can work with tissue “live” at the microscope, or
from image stacks taken from tissue sections. Non-stereological
quantifi cation of OI in tissue section stacks, using standard light or
fl uorescent microscopy, has certain limitations and leads to sampling
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