Stereo Investigator

Count cells and quantify lengths, areas, and volumes with the world's best and most-cited stereology system

A Stereo Investigator® system for stereology gives you 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 helped lead 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.

Stereology with Stereo Investigator can be done on a microscope system or from image stacks acquired in a manner suitable for stereology.

Visit to learn more about stereology

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.

Stereology on a Microscope

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


Stereo Investigator works with brightfield, multi-channel fluorescence, confocal, and structured illumination microscopes.  

Microscope hardware and Stereo Investigator software work in harmony to deliver a powerful, seamless stereology system. A typical system includes a microscope, computer, and Stereo Investigator software. Most of what is visible through the oculars is displayed on the computer screen. 

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

  • direct motorized stages to automatically move for systematic random sampling of tissue specimen
  • 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



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.

Customer Reviews

"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
"We've used Stereo Investigator for 10+ years. The technical support is outstanding, and the company itself is highly responsive to their customers."
Glenn Rosen, Ph.D.
Harvard Medical Center
"Stereo Investigator is the gold standard for unbiased stereology, and I can't say enough to praise the technical support provided by MBF Bioscience."
Bob Jacobs, Ph.D.
Colorado College

Stereo Investigator has been cited in over 6,000 published research papers. 

5 times more than its nearest competitor.


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

Stereo Investigator can quickly and easily create whole slide images of your entire specimen in 2D or 3D with the addition of the 2D and 3D Slide Scanning modules. The system is fully integrated and works unattended, allowing you to focus on other projects. Stereo Investigator directs the motorized stage, camera, and, for fluorescent images, the filter wheels and mirror cubes so there is no need for manual intervention. 

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 if the chosen probe does not require systematic random sampling, such as Cavalieri probe for regional area and volume, and Area Fraction Fractionator for calculating the area of a small subregion (such as lesions or plaques) within a larger region.










Newly redesigned Stereo Investigator version 2018

State of the art software for state of the art research

Case Studies

Thousands of research labs use Stereo Investigator to collect accurate, reproducible analyses. Read about some of their research on our blog.

Read Case Studies


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)


Media Library

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

Still Have Questions? Just Ask!