Stereo Investigator

Stereo Investigator®

Count Cells and Quantify Lengths, Areas, and Volumes with the World's Best and Most-Cited Stereology System

A Stereo Investigator system provides you with accurate, unbiased estimates of the number, length, area, and volume of cells or biological structures in a tissue specimen. It is a key research tool that has led to advances in numerous areas of neuroscience including neurodegenerative diseases, neuropathy, memory, and behavior, as well as other research fields including pulmonary research, spinal cord research, and toxicology.

With Stereo Investigator, stereology can be done on a microscope system  from image stacks, or from whole slide images. Visit to learn more about stereology.

No Bottom Padding


Stereo Investigator Works with Brightfield, Multi-Channel Fluorescence, Confocal, and Structured Illumination Microscopes

Stereo Investigator software includes sophisticated computerized microscope control that is powerful, flexible, and easy to use. The software and microscope hardware work together harmoniously, setting the standard in the state-of-the-art in stereology systems. A typical system includes a microscope, computer, and Stereo Investigator software.  

Stereo Investigator fully integrates with your microscope and associated hardware to reduce manual work and to speed up data collection. It can:

  • direct motorized microscope stages to automatically move in order to perform systematically random sampling of tissue specimens
  • control cameras so you can view live images or collect and save images and image stacks, even change or save camera settings for future use
  • control the focus position, change objective lenses or adjust the condenser
  • automatically change filter wheels and mirror cubes when acquiring fluorescent images or image stacks
  • it can support almost all file formats


Introduction to: Stereo Investigator and Unbiased Stereology


Stereo Investigator is the leading stereology software in the world. Watch the video and discover how Stereo Investigator can take your research to the next level!

Fully Integrated Microscope Systems

In addition to stereology software, a Stereo Investigator system includes any hardware you need, such as a microscope, computer, motorized stage, camera, etc., and comes with MBF’s technical support for the entire system as well as research support to optimize your experimental design.

No Bottom Padding

Stereology on a Microscope

Maximum functionality in fully integrated microscope system
Reduces work and speeds up data collection

Customer Reviews

"Stereo Investigator is the most reliable tool for collecting unbiased stereology data. It’s backed by excellent technical and research support teams at MBF."
Mark West, M.D., Ph.D.
Aarhus University, Denmark
"We have used Stereo Investigator for over 10 years now. The service and technical support is always great and they keep adding new updates with more tools."
Paula Bickford, Ph.D.
University of South Florida
"Stereo Investigator is an excellent research tool for unbiased stereology. In our research group when we set out to quantify the complex network nerves residing in the stomach mucosa. With Stereo Investigator we were able to get accurate estimates of numbers and show differences between your study groups without the introduction of sampling bias."
Mona Selim, Research Associate
University of Minnesota
"If there is another program for unbiased stereology, I don't know what it is. This is the gold standard, and I can't say enough to praise the technical support provided by MBF Bioscience."
Bob Jacobs, Ph.D.
Colorado College


Can I Upgrade my Existing Microscope Hardware?

  • There are two main options when purchasing a Stereo Investigator system:

1.Purchase a brand new system: We work with all the leading microscope manufacturers including:

● Zeiss Axio Imager M2/Z2
● Olympus BX53/BX63
● Leica DM4/DM6
2. Upgrade existing microscope hardware
  • We typically provide complete turn-key systems include all of the hardware, software and services you will need for your new system.  
  • If you already have an existing microscope, motorized stage, or camera that you would like to use in a new system, we are happy to help you determine if it would be appropriate to integrate it into a new system rather than purchase all new hardware. 
  • All of our Stereo Investigator systems are custom configured based on the specific research needs of each customer.  

Contact Us



Stereo Investigator is used in leading research labs and projects around the world.

Request a Quote


CBS 60 Minutes correspondent, Scott Pelley, and Dr. Daniel Perl of the Uniformed Services University of the Health Sciences, sit down to discuss how brain tissue scarring occurs after blast waves. Dr. Perl is shown using a customized MBF Bioscience microscope system for his research that is 1000x more powerful than an MRI.


Upgrade to the World's Most Cited Stereology System Today!

Switching to Stereo investigator from your current stereology system has never been easier. With an intuitive and task-oriented interface, Stereo Investigator offers researchers more functionality than any other stereology software. By upgrading today save up to 10% on your new stereology system, Stereo Investigator!

Make the Switch



Stereo Investigator has been Cited in Over 8,000 Published Research Papers. 

5 times more than its nearest competitor.



Slide Scanning Workflow

A completely new slide scanning workflow is easier to use, will save time training new users and give you great slide scanning results. Use this workflow to scan at any magnification and create high resolution 2D images or 3D stacks. This workflow brings all the controls and features necessary to complete slide scanning into one location.  Feature includes:

  • An easy-to-follow guide that makes it simple for new users to scan great quality images 
  • Background correction to insure clean, even, image quality
  • Heat map allows you to spot folds and other areas that need additional focus sites
  • Validate your settings before you start a long acquire by taking a test image

Stereology from Image Stacks

Performing stereology at the microscope from fluorescent tissue specimens can be problematic since exposure to light degrades fluorescent tissue. With Stereo Investigator you can acquire image stacks using systematic random sampling (SRS) - a method that produces image stacks suitable for stereology- and then perform stereology on the image stacks. A great benefit of stereology on image stacks is that you can run many probes for different types of analyses and never have to worry that your tissue will fade. Plus, it's easier to double check the analysis.

During SRS image stack acquisition, Stereo Investigator directs the motorized stage, camera, and, for fluorescent images, the filter wheels and mirror cubes. This means you can automatically capture image stacks at each sample site, and then take the image stacks to a computer with Stereo Investigator Desktop and perform stereological analysis. 

Read about how to analyze tissue cleared with CLARITY, SeeDB, 3DISCO, and more


Stereology on Whole Slide Images

Whole slide images give you the freedom to perform stereology on a computer away from the microscope. Stereology on 2D whole slide images can be employed for counting cells with the Physical Fractionator, quantifying area and volumes with the Cavalieri probe, and for calculating the area of a small objects, such as lesions or plaques, within a larger region using the Area Fraction Fractionator.



Stereo Investigator - Whole Slide Edition


Stereology on Cleared Tissue Specimens

Stereo Investigator – Cleared Tissue Edition is the gold standard in unbiased stereology for use on cleared tissue. It allows researchers to use the world’s most cited stereology software to analyze intact, cleared tissue specimens imaged with light sheet or confocal microscopes.




Stereo Investigator - Cleared Tissue Edition


Stereology Stand-Alone Software Solutions


Each Stereo Investigator System We Configure is:

  • Based upon your specific research needs.
  • Fully integrated - Stereo Investigator controls motorized stages, cameras, filter wheels etc.
  • Scalable, so it fits your budget and allows room for additional capabilities via our imaging modules and hardware upgrades.
  • Supported by our team of scientists and technicians who are experts in stereology, research software and laboratory hardware.
  • Our scientists can help you design your study.
  • Upgradable to new software versions that are released regularly.
Stereo Investigator has been developed with support form the National Institute of Mental Health (NIMH)



Professional Technical Support

When you call us you will speak with a person - not an automated system. Talk to us about your hardware, software, or experimental design questions. Our team includes Ph.D. neuroscientists and experts in microscopy, stereology, neuron tracing, and image processing; ready to help you over the phone or online.

Contract Services for Stereology

Our Stereology services allows university, pharmaceutical, biotechnical, or government laboratories to have the industry-leading experts perform unbiased stereology data collection and analysis for you. This allows researchers,  the ability to increase the rate and efficiency of your data collection. Whether it is brain, lung, or other biological tissue, you will get the accurate results you need. MBF Bioscience’s trusted staff has the equipment and the stereological expertise to handle all types of studies from small pilot studies to full-scale experimental analyses and prepare a comprehensive report for you.

Request More Information


MBF Bioscience Forum

Get answers to your most pressing research and technical questions from MBF scientists and fellow researchers.


Visit MBF Bioscience Forum


Watch These Webinars About Stereo Investigator

Webinar: Introduction to Stereo Investigator
Introduction to Stereo Investigator
Unbiased Stereology Question and Answer Session with MBF Bioscience
Unbiased Stereology Question and Answer Session with MBF Bioscience
What is Bias?
What is Bias?
Staining for Stereology Q&A webinar with Dr. Susan Tappan
Staining for Stereology Q&A
Stereology Question & Answer Webinar
Stereology Q&A session
Stereology concepts & probe selection - Webinar
Stereology Concepts & Probe Selection

We can also custom develop for you

MBF is proud to help bioscience leaders and experts push the next wave of innovation and discovery to benefit humanity. Given this, it’s possible you’re looking for customized technology for your needs. If that is the case, click here to get in touch with us directly. We’d be happy and honored to see if we can create something together that will move all of us forward.

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