Stereo Investigator - Whole Slide Edition

Stereo Investigator®- Whole Slide Edition

Quantitative Analysis Using Stereology on Whole Slide Images

Design-based stereology is a set of data analysis methods that ensure integrity in the quantitative analysis of the size, shape, and number of objects in a tissue sample. Stereology produces results that are unbiased and more reliable than non-stereologic analyses. Stereo Investigator Whole Slide Edition is a specialized software application for analyzing whole slide image data accurately and efficiently.



The Whole Slide version of Stereo Investigator is optimized for whole slide images and has a user interface that has been honed to be efficient and easy to learn. 

Researchers use Stereo Investigator Whole Slide Edition to Perform Analysis of:

  • cell population number
  • fiber and capillary length 
  • area and volume of anatomical regions
  • area and volume of cells
  • area and volume fraction of Alzheimer plaques


Stereo Investigator Whole Slide Edition can Analyze Image Data Sets Acquired From:

For more information about stereological methods and their importance in histology analysis go to


Specially Designed Stereology Probes for Analyzing Whole Slide Images

There are numerous stereological probes included in Stereo Investigator Whole Slide edition for quantifying number, length, surface, volume, and area:


  • Physical Fractionator
  • Fractionator



  • Combined Point Intercept
  • Petrimetrics



  • Merz
  • Weibel
  • Cycloids for Sv
  • Sv-cycloid Fractionator


  • Area fraction fractionator 
  • Nucleator
  • Cavalieri estimator
  • Combined point intercept
  • Point sampled intercept
  • Surface-weighted star volume
  • Discrete vertical rotator

Second order:

  • Connectivity assay 





Some examples are shown below:

Quantify surface area per volume of gut smooth muscle layer with the Merz probe
The length of dendrites in culture is analyzed with petrimetrics
The percentage by volume of plaque in the cortex is analyzed with the area fraction fractionator probe
Quantify the area of the lumen and the boundary-length of the internal elastic lamina of the cross section of an artery with the combined point-intercept probe


Integrates with our Full Suite of Products

Get the most of whole slide images by scanning with the TissueScope slide scanner, to storing and sharing using our image management platform Biolucida, to reconstructing with the 3D BrainMaker, and analyzing using Neurolucida 360 (for automatic 3D neuron reconstruction) and Stereo Investigator Whole Slide Edition.

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Watch a Webinar where Drs. Dan Peruzzi and Nathan O’Connor introduce Stereo Investigator - Whole Slide Edition, designed specifically to perform unbiased stereology on large, whole slide images, and demonstrate probes. They also discuss data workflows, including whole slide scanning using our scanning technologies, and slide management using Biolucida.



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

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