Stereo Investigator - Cleared Tissue Edition

Stereo Investigator®  - Cleared Tissue Edition

Accurate, Unbiased Stereology for Cleared Tissue

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 — MBF Bioscience’s Stereo Investigator — to analyze intact, cleared tissue specimens imaged with light sheet or confocal microscopes.

Systematic Random Sampling throughout the user defined region of interest, and marking just cell tops contained within the counting frames, ensures accurate unbiased results.

No Padding

Customer Reviews

Stereo Investigator Cleared Tissue edition is great! We used it on large light-sheet datasets obtained from human brains with 4-channel imaging for different markers of neuronal populations. We could obtain cell type-specific stereologic data from a cytoarchitecturally defined region of the neocortex. We then registered the entire stereologic dataset, including laminar boundaries and sampled cells, to a high-resolution MRI dataset.
Patrick R. Hof, Ph.D.
Icahn School of Medicine at Mount Sinai
"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 it highly responsive to their customers."
Glenn Rosen, Ph.D.
Harvard Medical Center
"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

Introduction to: Stereo Investigator - Cleared Tissue

Researchers around the world trust Stereo Investigator - Cleared Tissue for their unbiased stereology needs on both confocal and light sheet microscopes. Watch the video to see how it works!

Stereo Investigator – Cleared Tissue Edition is software specifically engineered for analyzing cleared tissue image data accurately and efficiently. It includes the Image Volume Fractionator, a new, state-of the-art stereological probe developed by MBF Bioscience to count cells in large, 3D images of intact specimens.

  • Quantifies:
• Numbers of cells
• Cell volume and surface area
• Length of branching structures
• Region volumes and surface areas
  • Reads image files produced by most light sheet and confocal microscopes
  • High-performance 3D visualization
  • Intuitive workflows make it easy to learn and use

Specially Designed Stereology Probes for Analyzing Cleared Tissue

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.

Traditional unbiased stereology was created to accurately quantify tissue sections. We developed new, innovative technology, Stereo Investigator – Cleared Tissue Edition to solve the unique challenges inherent in working with large intact cleared tissue or thick slabs of cleared tissue specimens.

There are numerous stereological probes included in Stereo Investigator Cleared Tissue Edition for quantifying number, length, surface, volume, and area:


  • Image Physical Fractionator


  • Image Volume Spaceballs
  • Cycloids for Lv


  • Area Fraction Fractionator
  • Nucleator
  • Cavalieri Estimator
  • Planar Rotator
  • Optical Rotator


  • Isotropic Fakir
  • Surfactor
  • Optical Rotator



Researchers use Stereo Investigator Cleared Tissue Edition to perform analysis of:

  • Cell populations
  • Cell size, area, volume, surface
  • Fiber or capillary lengths
  • Area or volume for regions of interest

Stereo Investigator Cleared Tissue can Analyze Image Data Sets Acquired From:

  • ClearScope
  • Zeiss
  • Hamamatsu
  • Leica
  • Olympus
  • and more...


Stereology Stand-Alone Software Solutions

Request a Quote



Compatible with Many Tissue Clearing Techniques

  • Scal
  • uDISCO
  • CUBIC 
  • SeeDB 


Works with Big Image Data from Most Research Microscope Imaging Systems


  • Confocal
  • Light sheet
  • Two-photon
  • Fluorescence
  • Slide scanners 

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.

MBF Bioscience Forum

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


Visit MBF Bioscience Forum


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.

Still Have Questions? Just Ask!

Paragraphs Contact Form

This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.