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 10/04/2016.

starindicates that the researchers did a good job reporting stereological parameters

Sleep and serotonin modulate paracapsular nitric oxide synthase expressing neurons of the amygdale

Synaptic Vesicle Protein 2A as a Novel Pharmacological Target with Broad Potential for New Antiepileptic Drugs

Chemogenetic Activation of an Extinction Neural Circuit Reduces Cue-Induced Reinstatement of Cocaine Seeking

EphrinB3 restricts endogenous neural stem cell migration after traumatic brain injury

The potential role of amlodipine on experimentally induced bacterial rhinosinusitis

Immature neurons and radial glia, but not astrocytes or microglia, are altered in adult Cntnap2 and Shank3 mice, models of autism | eNeuro

Physical exercise induces structural alterations in the hippocampal astrocytes: exploring the role of BDNF-TrkB signaling

Uncoupling protein 2 modulation of the NLRP3 inflammasome in astrocytes and its implications in depression

Glucose intolerance after chronic stress is related with downregulated PPAR-γ in adipose tissue

DCC confers susceptibility to depression-like behaviors in humans and mice and is regulated by miR-218

The effect of unilateral disruption of the centrifugal visual system on normal eye development in chicks raised under constant light conditions

Neuroprotective and immunomodulatory effects of raloxifene in the myenteric plexus of a mouse model of Parkinson’s disease

Adult Conditional Knockout of PGC-1α Leads to Loss of Dopamine Neurons

Dopaminergic Neurodegeneration in the Mouse Is Associated with Decrease of Viscoelasticity of Substantia Nigra Tissue

Graphene quantum dots conjugated neuroprotective peptide improve learning and memory capability

Trophic factors intervention regenerates the nestin-expressing cell population in a model of perinatal excitotoxicity: Implications for perinatal brain injury and prematurity

Neuron density is decreased in the prefrontal cortex in Williams syndrome

Asymmetric Direct Reciprocal Connections Between Primary Visual and Somatosensory Cortices of the Mouse

Mitochondrial dysfunction in myofibrillar myopathy

A comparative study of sex difference in calbindin neurons among mice, musk shrews, and Japanese quails

Autophagy Inhibition Favors Survival of Rubrospinal Neurons After Spinal Cord Hemisection

Melatonin prevents radiation-induced oxidative stress and periodontal tissue breakdown in irradiated rats with experimental periodontitis

The human-specific CASP4 gene contributes to Alzheimer-related synaptic and behavioral deficits

CD38 Knockout Mice Show Significant Protection Against Ischemic Brain Damage Despite High Level Poly-ADP-Ribosylation

Midazolam–ketamine dual therapy stops cholinergic status epilepticus and reduces Morris water maze deficits

Lengths of nephron tubule segments and collecting ducts in the CD-1 mouse kidney: an ontogeny study.

Neurovascular unit remodelling in the subacute stage of stroke recovery

Effects of platelet-rich plasma on cartilage regeneration after costal cartilage resection: a stereological and histopathological study

Voluntary Running Exercise-Mediated Enhanced Neurogenesis Does Not Obliterate Retrograde Spatial Memory

High–Molecular-Weight Paired Helical Filaments from Alzheimer Brain Induces Seeding of Wild-Type Mouse Tau into an Argyrophilic 4R Tau Pathology in Vivo

Neonatal hepatitis B vaccination impaired the behavior and neurogenesis of mice transiently in early adulthood

NOX2 drives M1-like microglial/macrophage activation and neurodegeneration following experimental traumatic brain injury

Metformin Prevents Nigrostriatal Dopamine Degeneration Independent of AMPK Activation in Dopamine Neurons


Altered skeletal muscle (mitochondrial) properties in patients with mitochondrial DNA single deletion myopathy

Focused Ultrasound-Induced Neurogenesis Requires an Increase in Blood-Brain Barrier Permeability

Different Seasonal Patterns in Song System Volume in Willow Tits and Great Tits

Ingestion of dried-bonito broth (dashi) facilitates PV-parvalbumin-immunoreactive neurons in the brain, and affects emotional behaviors in mice


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 prepare your tissue accurately and efficiently.
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