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, stereology.info 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

Processor

4-core

CPU RAM

16 GB

GPU RAM

>6 GB

Recommended System Requirements

Operating System

Windows 10, 64-bit

Processor

8-core

CPU RAM

64 GB

GPU RAM

>8 GB

Storage

Solid state drive(s)

File Input Options

Supported image file formats

CZI, HDF5, H5, IMS, JP2, JPG, JPEG, JPF, MJC, JPX, LIF, LSM, ND2, OIB, OIF, TIF, TIFF, SVS

Output Specifications

Data output formats

XML*, ASC, DAT

 

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

Image file output formats

JP2, JPX, TIFF, SVG

Movie export format

MP4

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
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Stereo Investigator System for Quantifying Neurotransmitter Switching in Human Brains Installed at Dr. Nicholas Spitzer’s Lab
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Differences Associated with Fetal Growth Restriction are Found Using Stereo Investigator
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Curcumin Lowers Neuroinflammation in Mouse Model
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MBF Bioscience research team contributes novel dendritic spine analysis in study published in Science
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Diet Restriction Slows Neurodegeneration and Extends Lifespan of DNA-Repair-Deficient Mice
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Uncovering the role of microglia in fetal alcohol spectrum disorders
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Stereological Study Reveals Neuron and Glia Proliferation in Hippocampus of Lithium-Treated Mice
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Iron Deficiency Worsens Fetal Alcohol Spectrum Disorders
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Genetic Mutation Accelerates CTE Pathology
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Dying neurons in Alzheimer’s patients show signs of improvement after gene therapy
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How Transplanted Stem Cells Behave in Injured Spinal Cord Tissue
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Delayed loss of neurons occurs in mice with mild TBI and anxiety
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Higher levels of pTau found in Alzheimer’s disease patients with psychosis
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New Neurons Erase Memories
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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
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Exercise Heals the Brain After Binge Drinking
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Scientists use Stereo Investigator to Discover that Part of the Hippocampus Shrinks in Socially Isolated Rodents
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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
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New Zealand Scientists Use Stereo Investigator to Develop a New Model for Human Extreme Prematurity
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Scientists Assess Kidney Damage with Stereo Investigator, Determine Ultrasound Prevents Organ Injury
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Munich Scientists Analyze Placenta Morphometry with Stereo Investigator
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UCLA Scientists Count Cells with Stereo Investigator in Study Identifying Compensating Regions in Brain Damage
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Increased Choline During Pregnancy Improves Learning in Down Syndrome Mice
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Study Links Increased Touch to Enhanced Neurogenesis in Adult Mice; Stereo Investigator Used for Quantification
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Wisconsin Scientists Use Stereo Investigator to Quantify Neurons Formed From Stem Cells
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Researchers Use Stereo Investigator to Identify Abnormalities in Autistic Brains
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Neurolucida & Stereo Investigator Help Uncover Cerebellar Granule Cells’ Role in Muscle Memory
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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
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Florida Researchers Study Traumatic Brain Injury With Stereo Investigator
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MBF Contributes to Recent PLOS Article on New Mouse Model for Huntington’s Disease
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Scientists at Duke Say Mice Have Features Associated With Vocal Learning
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Stereo Investigator Helps Harvard Scientists Study Social Isolation’s Effects on the Brain
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Yale Researchers Make Breakthrough in Possible Depression Treatment
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UVM Scientists Use Neurolucida and Stereo Investigator to Study Neurons in the Avian Iris
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John Hopkins University Scientists Quantify Neurons with Stereo Investigator
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UCLA Scientists use Stereo Investigator to Quantify Juvenile Neurogenesis in Mice
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DHA Supplementation Prior to Brain Injury May Reduce Severity
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Washington University Researchers use Stereo Investigator to Study Axonal Transport in Parkinson’s Model
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University of Kansas Researchers use Stereo Investigator to Map Fetal Brain Hypoxia Sites
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Stereo Investigator Assists Stanford Stroke Center Scientists in Stem Cell Research
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Toronto Scientists Get First Direct Measurement of Myometrial SMCs in Pregnant Rat Uterus With Stereo Investigator
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Scientists in Spain Track Recovery in the Auditory Cortex
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Stereo Investigator Helps Uncover Autonomic Diabetic Neuropathy Link
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Yale Scientists Say AAV5 is Best for Transduction in Primates
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Mount Sinai Scientists Research the Effect of Aging on Learning and Memory with Stereo Investigator
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Stereo Investigator Helps Washington D.C. Scientists Study the Emergence of Human Language
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Swiss Scientists Use Stereo Investigator to Study Schizophrenia
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Stereo Investigator Aids in Researching Familial Alzheimer’s Disease
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Stem Cell Transplants Aid in Spinal Recovery
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Visit our blog to read more case studies

Download Stereo Investigator product sheet here.

 

Stereo Investigator® Version 2024.1.2
Released July 2024

New Features and Enhancements

  • New auto-calibration feature offers hands-free correction for camera rotation and establishes lens calibration
  • New Scan Repair for continuing incomplete slide scans and replacing problematic image tiles
  • Added the ability to Live Zoom or zoom in on the live-camera feed
  • Slide scanning workflow now includes the option to employ “Stitching” for improved alignment of adjacent images
  • Added the ability to conduct Parcentric Parfocal calibration of just a single objective
  • Slide Scanning added a new filter for background subtraction
  • New ability to set the rotation angle in 3D view
  • Biolucida integration
    • New image browser
    • Improved Biolucida connection interface
  • Added support for the new MBF Bioscience Vesalius Spinning disk confocal structured illumination device
  • Added support for Aura Light source and the 89 North LDI
  • Can now save a file containing a single color channel from a multi-color channel image
  • Added support for 12-bit OME-TIFF files

 

View Full Version History Here.

Our Range of Stereology Solutions

Feature Description

Stereo Investigator MICROSCOPE EDITION

Stereo Investigator DESKTOP EDITION

Stereo Investigator CLEARED TISSUE 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. 

Testimonials

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.
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  • 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.

Stereo Investigator® AI

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