The Most Comprehensive Source of Stereology Information on the Web

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


Recommended Readings

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Recent Noteworthy Stereology Publications

Published papers using unbiased stereology; last updated on 02.26.2024.

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

starPhenotypically concordant distribution of pick bodies in aphasic versus behavioral dementias

Rat Model of Type 2 Diabetes Mellitus Recapitulates Human Disease in the Anterior Segment of the Eye

Silencing Parkinson’s risk allele Rit2 sex-specifically compromises motor function and dopamine neuron viability

STING-dependent signaling in microglia or peripheral immune cells orchestrates the early inflammatory response and influences brain injury outcome

Differential expression of paralog RNA binding proteins establishes a dynamic splicing program required for normal cerebral cortex development 

Neonatal IL-4 Over-Exposure is Accompanied by Macrophage Accumulation in Dura Mater After Instant Anti-inflammatory Cytokine Response in CSF

The effects of Garcinia kola and curcumin on the dorsal root ganglion of the diabetic rat after peripheral nerve transection injury

Chronic traumatic encephalopathy and aging-related tau astrogliopathy in community-dwelling older persons with and without moderate-to-severe traumatic brain injury 

Microglial inhibition alleviates alpha-synuclein propagation and neurodegeneration in Parkinson’s disease mouse model

Immunoregulatory and neutrophil-like monocyte subsets with distinct single-cell transcriptomic signatures emerge following brain injury

Adult-Onset Deletion of ATP13A2 in Mice Induces Progressive Nigrostriatal 2 Pathway Dopaminergic Degeneration and Lysosomal Abnormalities


Phosphorylated α-synuclein deposited in Schwann cells interacting with TLR2 mediates cell damage and induces Parkinson’s disease autonomic dysfunction

Efficacy and safety of the regulatory T cell-selective interleukin-2 receptor agonist rezpegaldesleukin (REZPEG) in the treatment of inflammatory skin diseases including atopic dermatitis

Choice impulsivity after repeated social stress is associated with increased perineuronal nets in the medial prefrontal cortex

The choroid plexus maintains ventricle volume and adult subventricular zone neuroblast pool, which facilitates post-stroke neurogenesis

Accelerated neurodegeneration of basal forebrain cholinergic neurons in HIV-1 gp120 transgenic mice: Critical role of the p75 neurotrophin receptor

Antigen-specific age-related memory CD8 T cells induce and track Alzheimer’s-like neurodegeneration

IFNγ drives neuroinflammation, demyelination, and neurodegeneration in a mouse model of multiple system atrophy

starDopamine neuron degeneration in the Ventral Tegmental Area causes hippocampal hyperexcitability in experimental Alzheimer’s Disease

Neuroinflammatory gene expression profiles of reactive glia in the substantia nigra suggest a multidimensional immune response to alpha synuclein inclusions

Neurotrophin-3 from the dentate gyrus supports postsynaptic sites of mossy fiber-CA3 synapses and hippocampus-dependent cognitive functions

ROCK2 regulates microglia proliferation and neuronal survival after traumatic brain injury

Developmental exposure to methylmercury alters GAD67 immunoreactivity and morphology of endothelial cells and capillaries of midbrain and hindbrain regions of adult rat offspring

Ellagic Acid Prevents α-Synuclein Spread and Mitigates Toxicity by Enhancing Autophagic Flux in an Animal Model of Parkinson’s Disease

Kv3.1 voltage-gated potassium channels modulate anxiety-like behaviors in female mice

Intranasal insulin attenuates hypoxia-ischemia-induced short-term sensorimotor behavioral disturbances, neuronal apoptosis, and brain damage in neonatal rats

Amyloid-β specific regulatory T cells attenuate Alzheimer’s disease pathobiology in APP/PS1 mice

Bdnf-Nrf-2 crosstalk and emotional behavior are disrupted in a sex-dependent fashion in adolescent mice exposed to maternal stress or maternal obesity

CSF-1R inhibitor PLX3397 attenuates peripheral and brain chronic GVHD and improves functional outcomes in mice

Modulation of mitochondrial function with near-infrared light reduces brain injury in a translational model of cardiac arrest

Extracellular vesicles from hiPSC-NSCs can prevent peripheral inflammation-induced cognitive dysfunction with inflammasome inhibition and improved neurogenesis in the hippocampus

Pattern of ventral temporal lobe interconnections in rhesus macaques

Cardioprotective function of sclerostin by reducing calcium deposition, proliferation, and apoptosis in human vascular smooth muscle cells

Continue reading “Recent Noteworthy Stereology publications”


Date: July 19th, 2023

Webinar: Fluorescent Imaging and Slide Scanning – Techniques and Best Practice

Biosystems Specialist Jean Fecteau and Software and Hardware Support Engineer Jordan Deso host this webinar and delve into the principles of imaging fluorescent samples, as well as share best practices for utilizing our SlideScan Workflow with fluorescent samples.

Topics include:
  • Photochemistry of fluorescence
  • Introduction to the microscope fluorescent light path
  • Slide scanning concepts
  • Issues commonly encountered when imaging fluorescent samples
  • Typical applications of fluorescence and fluorescent slide scanning
Date: March 25th, 2021

Introduction to Stereo Investigator

Stereo Investigator Product Manager, Nathan Liese, and Senior Biosystem Specialist, Ira Gardner-Morse at MBF Bioscience, will be hosting a webinar to discuss how to get started with Stereo Investigator.

Topics include:
  • Basics of microscope integration
  • Getting familiar with the Stereo Investigator interface
  • Quantification using the Optical Fractionator Probe
  • Cavalieri Probe
  • Exporting results
  • Image acquisition and slide scanning
Date: April 21, 2020

Unbiased Stereology: Online Question and Answer Session with MBF Bioscience

Dr. Dan Peruzzi, stereology educator and staff scientist at MBF Bioscience, covers both theoretical and practical aspects regarding the use of unbiased stereology to quantify morphological parameters of tissue observed under a microscope or a slide scanner.

Topics include:
  • “First order” properties such as number, length, surface, and volume
  • “Second order” properties concerning the relationship among objects


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