The Most Comprehensive Source of Stereology Information on the Web

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Stereology Information for the Biological Sciences

This site introduces both basic and advanced concepts of Stereology. The emphasis is on the use of stereology in biological research, though anyone interested in learning concepts of stereology will find something of interest. The application of stereological methods to biological studies permits researchers to effectively and efficiently gather unbiased, accurate data. This site is dedicated to helping researchers understand the principles of design-based stereology and its advantages over less sophisticated approaches in quantitative histology.

What is Stereology?

Design-based stereology is a set of methods to ensure rigorous quantitative analysis of the size, shape, and number of objects. When properly used, stereology plays an important role in validating and rejecting experimental hypotheses in biological research. It produces results that are unbiased, efficient, and more reliable than other ad hoc quantitative analyses. Unbiased stereology provides an important contribution to the advancement in biological research by improving the consistency and dependability of quantitative analytical results produced in the laboratory and reported in scientific publications.

An Introduction to Stereology Probes

The most modern unbiased stereology probes are used to quantify aspects of biological tissue in a reproducible and efficient manner. These stereological probes are appropriate for many fields of basic and applied biological and medical research. These probes should always be used in conjunction with systematic random sampling.



Estimate the size of cell populations with the optical fractionator in thick tissue sections. In this probe, sub-volumes are sampled and then are extrapolated to arrive at an estimate of the entire cell population. A virtual space called an optical disector is used in thick sections that can be oriented anyway you like. Disector counting rules are followed to avoid overestimating, and an oil objective lens is employed for imaging, since fine z-resolution is needed to find the leading edge of the cell and to have enough focal planes to determine if it is in the disector. Note: avoid counting pieces of cells when you really want to count whole cells.    OPTICAL FRACTIONATOR


NUCLEATOR to estimate VOLUME of cells

Estimate individual cell volumnucleator-2es with the nucleator. A point in the cell is identified, then one to four rays are marked and their mean length is used in the formula for the volume of a sphere, generating an estimate of the cell volume. The volume estimate is number-weighted; the sampling is done with a disector in thick sections so that it is not more likely to sample larger cells than smaller cells. It is important to use a method to select cells without bias by picking them in a manner that does not favor any position of the cell in space; you won’t overestimate by sampling too many larger cross-sections or underestimate by sampling too many smaller cross-sections.    NUCLEATOR




This probe is versatile in that it can be used on thin optical or physical sections that are oriented according to the preference of the researcher. A fraction of the tissue is marked with points over the region(s) of interest, and an extrapolation is carried out to arrive at the estimate. Unbiased estimates of regional volume are easy to obtain efficiently using Cavalieri point-counting.     CAVALIERI/POINT-COUNTING


SPACEBALLS to estimate LENGTH of fibers and vessels


Estimate length of biological filaments such as axons or blood vessels without facing the herculean task of tracing them all. Instead the intersections of the filaments with a virtual sphere are marked and converted to a length estimate. Thick sections may be oriented as the researcher prefers. This probe is implemented along with the fractionator method; a volume-fraction is sampled and extrapolated using the reciprocal of the volume fraction to arrive at the estimate of length.    SPACEBALLS


ISOTROPIC FAKIR to estimate SURFACE of membranes


To estimate surface area, a triplet of line segments that has the property of being isotropic in space is used to probe in thick sections. Intersections of the triplet with the surface are counted and a formula is used to arrive at an estimate of the surface area; the more intersections recorded the greater the surface. Like the other regional probes on this page, thick, preferentially oriented sections are used and the fractionator method works to make an extrapolation based on the fraction of volume that was sampled.     ISOTROPIC FAKIR

more probes including solutions for thin tissue sections


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Recent Noteworthy Stereology Publications

Published papers using unbiased stereology; last updated on 05.23.2017.

starindicates that the researchers did a good job reporting stereological parameters. To see what parameters should be reported click here.

starFemale gonadal hormone effects on microglial activation and functional outcomes in a mouse model of moderate traumatic brain injury

Acute oligodendrocyte loss with persistent white matter injury in a third trimester equivalent mouse model of fetal alcohol spectrum disorder

Glutamine antagonist-mediated immune suppression decreases pathology but delays virus clearance in mice during nonfatal alphavirus encephalomyelitis

A high-fat diet can affect bone healing in growing rats

Effects of L-DOPA/benserazide co-treatment on colonic excitatory cholinergic motility and enteric inflammation following dopaminergic nigrostriatal neurodegeneration

Astrocytic expression of the RNA regulator HuR accentuates spinal cord injury in the acute phase

Possible effects of some agents on the injured nerve in obese rats: A stereological and electron microscopic study

Functional organization of the medial temporal lobe memory system following neonatal hippocampal lesion in rhesus monkeys

Enriched environment attenuates behavioral seizures and depression in chronic temporal lobe epilepsy

Reorganization of the septohippocampal cholinergic fiber system in experimental epilepsy

STN-DBS is neuroprotective in the A53T α-synuclein Parkinson’s disease rat model

Post-injury administration of a combination of memantine and 17β-estradiol is protective in a rat model of traumatic brain injury

Effects of environmental enrichment on the activity of the amygdala in micrencephalic rats exposed to a novel open field

Differential effects of immunotherapy with antibodies targeting α-synuclein oligomers and fibrils in a transgenic model of synucleinopathy

Complexity of Stomach–Brain Interaction Induced by Molecular Hydrogen in Parkinson’s Disease Model Mice

Spinal cord injury in hypertonic newborns after antenatal hypoxia-ischemia in a rabbit model of cerebral palsy

The Hawk-Eyed Songbird: Retinal Morphology, Eye Shape, and Visual Fields of an Aerial Insectivore

Remodeling the Th1 polarized systemic environment contributes to neurogenesis and cognitive function via the Wnt7a pathway in neonatal mice

Moderate-Grade Germinal Matrix Haemorrhage Activates Cell Division in the Neonatal Mouse Subventricular Zone

Ontogenetic changes in spectral sensitivity and retinal topography in the retina of the yellowtail kingfish (Seriola lalandi): Implications for the global Seriola aquaculture industry

Neuroprotective Effects of Temsirolimus in Animal Models of Parkinson’s Disease

Effects of bilateral vestibular deafferentation in rat on hippocampal theta response to somatosensory stimulation, acetylcholine release, and cholinergic neurons in the pedunculopontine tegmental nucleus

Motor deficits and beta oscillations are dissociable in an alpha-synuclein model of Parkinson’s disease

512 – shRNA-Based Suppression of Connexin 43 and Low Packing Density of Connexin 43 Immunoreactive Aggregates are Associated with Depression-Like Behavior in Rats

Continue reading “Recent Noteworthy Stereology publications”

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What’s New in

Added on 09.25.2015
Added on: 11.05.2015
Reviewed paper: Schmitz, C. and P.R. Hof (2005) Design-Based Stereology in Neuroscience. Neuroscience 130, 813-831. Added on: 03.10.2016
In 2014 researchers used Stereo Investigator in 698 peer-reviewed papers – citing it nearly 3x more than all other stereology systems combined.

Learn how to count cells in an unbiased manner with the Optical Fractionator probe in Stereo Investigator
Learn more about estimating your probe
Added on 04.10.2015

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developers of Stereo Investigator, the world’s most cited stereology system