Stereo Investigator®

The complete stereology solution. The world’s most widely cited system for unbiased cell counting
MBF Bioscience > Stereo Investigator®

Product Overview

A Stereo Investigator system provides you with the means to make the most accurate, unbiased quantification of the number, length, area, and volume of cells, subcellular and macro structures in your tissue specimens. It is a key research tool that has helped scientists to make discoveries in numerous areas of neuroscience, including neurodegenerative diseases, addiction, autism, neuropathy, memory, and behavior, as well as other research fields including pulmonary and kidney research, and toxicology.


The Stereo Investigator system makes stereology accessible, with easy-to-follow workflows for the most commonly used probes and clear quantitative results. With Stereo Investigator, stereology can be performed directly on a microscope system, or from image stacks or whole slide images.


Visit our comprehensive stereology information site, to learn more.

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Key Benefits

Stereology made accessible

With Stereo Investigator, you can perform unbiased quantification of cell populations, lengths of fibers or vessels, or area and volume of regions using design-based stereology, a set of methods for rigorous quantitative analysis of the size, shape, and number of objects. Stereo Investigator leverages unbiased statistical sampling, that helps enable researchers to count, measure, and precisely quantify visible features in microscope specimens using any of the 20+ included stereology probes without needing to examine the entire specimen to obtain statistically valid results. Stereo Investigator makes complicated stereological analyses simpler. It navigates you through the rigorous procedures required for unbiased quantitation or morphometric analyses and generates relevant calculations needed to generate final results and statistics. When needed or desired, you can also generate reviews and audits.

Stereo Investigator software includes sophisticated computerized microscope control that is powerful, flexible, and easy to use. In a complete Stereo Investigator system, which includes a microscope, computer, and Stereo Investigator software, all individual components work together harmoniously, setting the standard for state-of-the-art stereology systems.

Join the growing community of researchers who trust Stereo Investigator to help them obtain reliable results suitable for publication in high impact-factor journals over the last 20 years.  With more than 8,000 published research papers, Stereo Investigator is cited 5+ times more frequently than its nearest competitor. 

Stereo Investigator has been developed with support from the National Institute of Mental Health (NIMH)

Minimum System Requirements

Operating System

Windows 10, 64-bit




16 GB


>6 GB

Recommended System Requirements

Operating System

Windows 10, 64-bit




64 GB


>8 GB


Solid state drive(s)

File Input Options

Supported image file formats


Output Specifications

Data output formats



* Our XML data file format, the Neuromorphological File Specification (NFS), is endorsed as a standard by the INCF.

Image file output formats


Movie export format


Hardware Compatibility










Computer controlled microscopes

Leica supported microscopes:

  • DM6B
  • DM4
  • DM 3000
  • DM 4000
  • DM 4500
  • DM 5000
  • DM 5500
  • DM 6000
  • DM 6000-FS
  • DM 8000M
  • DM12000M
  • DM4
  • DM6
  • DMI4000
  • DMI 5000
  • DMI 6000
  • DMI8



Zeiss supported microscopes:

  • AxioImager 1 and 2 series
  • Vario
  • AxioVert 200M
  • Zeiss Axioplan/phot 2(i)(ie)


Nikon supported microscopes

  • 90i/80i
  • TE2000
  • Ti
  • Ni-U
  • Ni-E
  • Ci-E


Olympus BX and IX Series:

  • BX63
  • BX53
  • IX83
  • IX2/BX2 UCB control boxes

Manual microscopes

Most models after 2002 of Zeiss, Olympus, Nikon, Leica


Structured illumination

  • Zeiss Apotome I, II, III
  • Olympus DSU
  • CarvII
  • Optigrid

Filter wheels and shutters

Zeiss, Olympus, Leica, Nikon, LEP, Prior, Sutter




Color video cameras

  • Qimaging Retiga 2000R
  • Lumenera Lumen HR
  • Optronics Microfire
  • Zeiss Axiocam MRc, 305, 506, 512, 705, 712
  • DVC 2000C
  • Leica DFC
  • Basler



Monochrome video cameras

  • Hamamatsu
  • Zeiss Axiocam MRm, 305, 506, 512, 702, 705, 712?
  • Leica DFC
  • Cooke Sensicam QE, EM
  • Cooke PCO

Light sources

  • Lumencore Sola
  • X-Cite 120PC, 120LED, Exacte, XYLIS, XLED1, TURBO, NOVEM

Supported Image File Formats: PDF

Contact us for an up-to-date list or question about specific models

Unprecedented study reveals structure-function adaptations in the facial nucleus of elephants
>> Learn More

Stereo Investigator System for Quantifying Neurotransmitter Switching in Human Brains Installed at Dr. Nicholas Spitzer’s Lab
>> Learn More

Differences Associated with Fetal Growth Restriction are Found Using Stereo Investigator
>> Learn More

Curcumin Lowers Neuroinflammation in Mouse Model
>> Learn More

MBF Bioscience research team contributes novel dendritic spine analysis in study published in Science
>> Learn More

Diet Restriction Slows Neurodegeneration and Extends Lifespan of DNA-Repair-Deficient Mice
>> Learn More

Uncovering the role of microglia in fetal alcohol spectrum disorders
>> Learn More

Stereological Study Reveals Neuron and Glia Proliferation in Hippocampus of Lithium-Treated Mice
>> Learn More

Iron Deficiency Worsens Fetal Alcohol Spectrum Disorders
>> Learn More

Genetic Mutation Accelerates CTE Pathology
>> Learn More

Dying neurons in Alzheimer’s patients show signs of improvement after gene therapy
>> Learn More

How Transplanted Stem Cells Behave in Injured Spinal Cord Tissue
>> Learn More

Delayed loss of neurons occurs in mice with mild TBI and anxiety
>> Learn More

Higher levels of pTau found in Alzheimer’s disease patients with psychosis
>> Learn More

New Neurons Erase Memories
>> Learn More

Scientists Use Stereo Investigator in Spinal Cord Injury Study
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Scientists Use Stereo Investigator in Spinal Cord Injury Study
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Scientists Map Photoreceptor Cells of Deep-Sea Sharks
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Humans Generate Most Cerebellar Granule Cells Postnatally
>> Learn More

Exercise Heals the Brain After Binge Drinking
>> Learn More

Scientists use Stereo Investigator to Discover that Part of the Hippocampus Shrinks in Socially Isolated Rodents
>> Learn More

Researchers from Quebec Delay Symptoms of Huntington’s Disease in Mouse Model
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Hawaii Scientists Measure Density of Parvalbumin-Interneurons With Stereo Investigator
>> Learn More

New Zealand Scientists Use Stereo Investigator to Develop a New Model for Human Extreme Prematurity
>> Learn More

Scientists Assess Kidney Damage with Stereo Investigator, Determine Ultrasound Prevents Organ Injury
>> Learn More

Munich Scientists Analyze Placenta Morphometry with Stereo Investigator
>> Learn More

UCLA Scientists Count Cells with Stereo Investigator in Study Identifying Compensating Regions in Brain Damage
>> Learn More

Increased Choline During Pregnancy Improves Learning in Down Syndrome Mice
>> Learn More

Study Links Increased Touch to Enhanced Neurogenesis in Adult Mice; Stereo Investigator Used for Quantification
>> Learn More

Wisconsin Scientists Use Stereo Investigator to Quantify Neurons Formed From Stem Cells
>> Learn More

Researchers Use Stereo Investigator to Identify Abnormalities in Autistic Brains
>> Learn More

Neurolucida & Stereo Investigator Help Uncover Cerebellar Granule Cells’ Role in Muscle Memory
>> Learn More

Stereo Investigator Contributes to Study Showing Low Zinc Levels Associated With More Cell Deaths in Spinal Cord Injury
>> Learn More

Stereo Investigator Helps Scientists Assess Damage in Rat Model of Ischemic Stroke
>> Learn More

Florida Researchers Study Traumatic Brain Injury With Stereo Investigator
>> Learn More

MBF Contributes to Recent PLOS Article on New Mouse Model for Huntington’s Disease
>> Learn More

Scientists at Duke Say Mice Have Features Associated With Vocal Learning
>> Learn More

Stereo Investigator Helps Harvard Scientists Study Social Isolation’s Effects on the Brain
>> Learn More

Yale Researchers Make Breakthrough in Possible Depression Treatment
>> Learn More

UVM Scientists Use Neurolucida and Stereo Investigator to Study Neurons in the Avian Iris
>> Learn More

John Hopkins University Scientists Quantify Neurons with Stereo Investigator
>> Learn More

UCLA Scientists use Stereo Investigator to Quantify Juvenile Neurogenesis in Mice
>> Learn More

DHA Supplementation Prior to Brain Injury May Reduce Severity
>> Learn More

Washington University Researchers use Stereo Investigator to Study Axonal Transport in Parkinson’s Model
>> Learn More

University of Kansas Researchers use Stereo Investigator to Map Fetal Brain Hypoxia Sites
>> Learn More

Stereo Investigator Assists Stanford Stroke Center Scientists in Stem Cell Research
>> Learn More

Toronto Scientists Get First Direct Measurement of Myometrial SMCs in Pregnant Rat Uterus With Stereo Investigator
>> Learn More

Scientists in Spain Track Recovery in the Auditory Cortex
>> Learn More

Stereo Investigator Helps Uncover Autonomic Diabetic Neuropathy Link
>> Learn More

Yale Scientists Say AAV5 is Best for Transduction in Primates
>> Learn More

Mount Sinai Scientists Research the Effect of Aging on Learning and Memory with Stereo Investigator
>> Learn More

Stereo Investigator Helps Washington D.C. Scientists Study the Emergence of Human Language
>> Learn More

Swiss Scientists Use Stereo Investigator to Study Schizophrenia
>> Learn More

Stereo Investigator Aids in Researching Familial Alzheimer’s Disease
>> Learn More

Stem Cell Transplants Aid in Spinal Recovery
>> Learn More


Visit our blog to read more case studies

Download Stereo Investigator product sheet here.


Stereo Investigator® Version 2023.1.2
Released April 2023

New Features and Enhancements

  • Added support for Leica K5 and K3C cameras’

  • Decimal points can now be entered during setup in the Slide Scanning workflow
  • Smart optimization feature is off by default


View Full Version History Here.

Our Range of Stereology Solutions

Feature Description

Stereo Investigator MICROSCOPE EDITION

Stereo Investigator DESKTOP EDITION


The gold standard for unbiased stereology
Quantifies number, length, volume, & surface area of cells, structures, & regions
Works with 3D images
Analyzes large 3D images aquired from light sheet and confocal microscopes
Works with 2D images
Analysis with images acquired from slide scanners
Integrated microscope control to work directly with live images at the microscope
Acquire 3D/2D images for Systematic Random Sampling (SRS)

Who Is Using Stereo Investigator?

Stereo Investigator is used across the globe by the most prestigious laboratories. 

News About Stereo Investigator

Cited in Peer Reviewed Scientific Publications

Stereo Investigator has been cited in over 8,000 published research papers. 5 times more than its nearest competitor.

Frequently Asked Questions (FAQ)

Do I need a microscope to run Stereo Investigator?

Most Stereo Investigator systems are microscope based.  It’s often fastest and easiest to evaluate specimens directly on the microscope.  We also offer the Stereo Investigator Desktop Edition that does not include microscope-control elements. With the desktop edition, you simply open previously acquired 2D images or 3D image stacks and perform the probe away from the microscope, freeing up the microscope for other uses. 

Can I use my existing microscope with Stereo Investigator?

Stereo Investigator can integrate with all 4 major microscope manufacturers (Zeiss, Olympus, Leica, and Nikon), but depending on your microscope model, components, and experimental needs, your current microscope configuration might require upgrades or selective substitution of components. Some of the most critical components are stage, focus drive, cameras, and light sources.  Please contact us to assess the compatibility of your existing microscope hardware and help you configure the optimal Stereo Investigator system for your research. 

Which MBF software modules enhance the capture & clarity of microscopic imaging process in Stereo Investigator Microscope Edition?

The following MBF software modules require Stereo Investigator to function and can help improve your microscopic imaging process:


  • 2D Slide Scanning Module allows you to create extremely high-resolution montages composed of images obtained from multiple microscopic fields-of-view. The resolution of the individual fields is maintained in the montage, allowing for the capacity to zoom in and out without loss of resolution. You can also combine high magnification detail resolution with a large field of view that is provided by lower power objectives. Scan the entire slide, or only specified sections or regions of interest within a section.


  • 3D Slide Scanning Module allows you to create 3D (focusable) Virtual Tissue images. This module also includes the 2D Slide Scanning  module. 


  • 3D Serial Section Reconstruction Module allows you to create 3D models from serial sections, align serial sections swiftly and precisely and implement shrinkage correction


  • Image Montaging Module allows you to automatically align and stitch together previously acquired 3D image stacks or 2D images to create a high resolution 3D montage of a region of interest


  • Image Stack Module allows you to acquire and analyze confocal, brightfield and widefield fluorescence 3D image stacks. It also adds the capability to create and export brightfield and widefield fluorescence image stacks to Stereo Investigator offline workstations, and includes 3D image visualization.


  • MRI Extension Module allows you to analyze 3D MRI images
What’s the difference between the desktop edition and the microscope edition?

Stereo Investigator: Microscope Edition is the most versatile and comprehensive version. It enables you to perform stereology directly on a microscope by controlling your microscope components, such as the motorized stage and camera. In addition to running nearly all stereological probes, you can document your experiments by acquiring images with sample and region localization so that it is easier to navigate and record your experiment.

Stereo Investigator: Desktop Edition has all the same probes as Microscope Edition, but is intended for use away from the microscope.  With this version, you can work from 2D images or 3D image stacks acquired previously. This frees up busy microscopes for other users and uses.  

Can I reconstruct things in 3D in Stereo Investigator?

Yes!  In addition to stereological analysis, Stereo Investigator offers the 3D Serial Section Reconstruction module. This enables you to map and reconstruct your regions of interest, view your data in 3D, and create and export movies or models for presentations. 


Robust Professional Support

Our service sets us apart, with a team that includes Ph.D. neuroscientists, experts in microscopy, stereology, neuron reconstruction, and image processing.  We’ve also developed a host of additional support services, including:

  • Forums
    We have over 25 active forums where open discussions take place.
    >> Learn More
  • On-Site/Training
    We’ve conducted over 750 remote software installations.
    >> Learn More
  • Webinars
    We’ve created over 55 webinars that demonstrate our products & their uses.
    >> Learn More

Request an Expert Demonstration

We offer a free expert demonstration of Stereo Investigator. During your demonstration you’ll also have the opportunity to talk to us about your hardware, software, or experimental design questions with our team of Ph.D. neuroscientists and experts in microscopy, neuron tracing, and image processing.

Related Products

Stereo Investigator® Cleared Tissue Edition

The gold standard in unbiased stereology for use on cleared tissue.


Automatic, accurate, unbiased, high-throughput cell quantification in histological specimens.

Recorded Webinars and Videos

Webinar: Discover the Optimal Sampling 'Sweet Spot' for Your Stereology Studies

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

Introduction to: Stereo Investigator and Unbiased Stereology