Stereo Investigator®– Cleared Tissue Edition

The gold standard in unbiased stereology for use on cleared tissue
MBF Bioscience > Stereo Investigator®– Cleared Tissue Edition

Product Overview

Stereo Investigator-Cleared Tissue Edition 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. Researchers around the world trust Stereo Investigator Cleared Tissue Edition for their unbiased stereology needs, including quantification of cell number, fiber length, and regional volumes and areas.

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Key Benefits

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, and even MicroCT. The program reads image files produced by most light sheet and confocal microscopes including ClearScope, Zeiss, Hamamatsu, Leica, Olympus, and more.

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’ve developed a new method in Stereo Investigator Cleared Tissue Edition to solve the challenges inherent in working with large intact cleared tissue or thick slabs of cleared tissue. Image Volume Fractionator is a new, state-of-the-art stereological probe developed by MBF Bioscience to count cells in large, 3D images of intact specimens.

Along with the Image Volume Fractionator, there are numerous stereological probes included in Stereo Investigator-Cleared Tissue Edition for quantifying number, length, surface, volume, and area. These include the following:

 

Number Length
  • Image Volume Fractionator
  • Image Volume Spaceballs
  • Cycloids for Lv
Volume/Area Surface
  • Area Fraction Fractionator
  • Nucleator
  • Cavalieri Estimator
  • Planar Rotator
  • Optical Rotator
  • Isotropic Fakir
  • Surfactor
  • Optical Rotator
Recommended Hardware Requirements
8-Core processor
Configured with 64GB of RAM
NVIDIA 1060 graphics card (1060=6GB)
Windows 10 OS
Compatible with the following file formats
  • JP2
  • TIF
  • BTF
  • LSM
  • CZI
  • H5
  • OIB
  • OIF
  • LIF
  • And more!

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
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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

 

Visit our blog to read more case studies

Download Stereo Investigator - Cleared Tissue Edition product sheet here

Stereo Investigator® - Cleared Tissue Edition 2022 Release Notes
Released February 2023

New Features and Enhancements:

  • Added ability to create a single section in the serial section manager for support of counting cut slabs of tissue 
  • Improvements in parameter reporting for Image Volume Fractionator and Image Volume Spaceballs 

 

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 - Cleared Tissue Edition?

Stereo Investigator – Cleared Tissue Edition is used across the globe by the most prestigious laboratories. 

News About Stereo Investigator - Cleared Tissue Edition

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)

Will the program work with different tissue clearing techniques?

Yes, the program is compatible with many tissue clearing techniques including CLARITY, iDISCO, uDISCO, SeeDB, Scale, and CUBIC.

What kind of images will the software work with?

The software will work with big image data from most research microscope imaging systems including light sheet, confocal, confocal resonant scanning, two-photon, and fluorescence.

What types of analyses can I perform with Stereo Investigator - Cleared Tissue Edition?

Researchers use Stereo Investigator - Cleared Tissue Edition to perform quantitative analysis of cell populations, cell area and volume, fiber or capillary length, and area and volume of regions of interest.

What’s the difference between Stereo Investigator and Stereo Investigator - Cleared Tissue Edition?

Both programs allow researchers to obtain quantitative data from tissue specimens. However, Stereo Investigator is for use with physical sections that have been cut on cryostats or microtomes, while Stereo Investigator Cleared Tissue Edition has been tailored to accommodate images that contain an entire region of interest acquired from intact cleared tissue.

Do I need an image of an entire organ to use the software?

No, you can use Stereo Investigator Cleared Tissue Edition with an image of a smaller region of interest within an organ, for example, the caudate putamen of the brain, as long as the entire region of interest is contained in the image.

Do you have a complete solution for cleared tissue imaging and stereology?

Yes, you can pair ClearScope, MBF Bioscience’s complete light sheet theta microscope system with Stereo Investigator Cleared Tissue Edition for a complete acquisition to quantitative data analysis pipeline.

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.
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  • 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.
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Request an Expert Demonstration

We offer a free expert demonstration of Stereo Investigator – Cleared Tissue Edition. 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.

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