Stereo Investigator – Whole Slide Edition is a specialized software application that allows researchers to use the world’s most cited stereology software – MBF Bioscience’s Stereo Investigator – to analyze 2D whole slide images accurately and efficiently using unbiased stereology. Stereo Investigator Whole Slide Edition has been tailored to 2D image data acquired from most slide scanners and microscope acquisition systems, and contains analyses for quantification of object number, fiber length, volume, and area.
Accurate Unbiased Stereology for Whole Slide Images
Stereo Investigator - Whole Slide Edition is the gold standard in unbiased stereology for use on 2D whole slide images. Design-based stereology is a set of data analysis methods that ensure integrity in the quantitative analysis of the size, shape, length, and number of objects in a tissue sample. Stereology produces results that are unbiased and more reliable than non-stereologic analyses. 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.
The software works with all 2D microscope images, but is an attractive solution if you work mostly, or exclusively with slide scanners, since it has been specifically designed for analyzing large whole slide images. Stereo Investigator - Whole Slide Edition is compatible with industry standard slide scanning formats and integrates seamlessly with Biolucida, our image serving platform. This allows for organized storage of images and easy collaboration between labs.
Stereo Investigator Whole Slide Edition can analyze image data sets acquired from TissueScopeTM and Microlucida® slide scanners, Zeiss, Leica, Olympus, Huron, Hamamatsu, Aperio and more! Researchers use Stereo Investigator Whole Slide Edition to perform many types of stereological analysis. Some examples include cell population number, fiber and capillary length, area and volume of anatomical regions, area and volume of cell, and number and size of Alzheimer’s plaques. There are numerous stereological probes included in Stereo Investigator - Whole Slide Edition, including the following:
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| Recommended Hardware Requirements |
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| 8-Core processor |
| Configured with 64GB of RAM |
| NVIDIA 1060 graphics card (1060=6GB) |
| Windows 10 OS |
| Compatible with the following file formats |
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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 - Whole Slide Edition product sheet here.
Stereo Investigator® - Whole Slide Edition 2023.1.1
Released February 2023
New Features and Enhancements:
View Full Version History Here.
The Area and Volume of any region of interest can be analyzed quickly, easily, and accurately using Cavalieri’s method of point counting.
The length of dendrites in culture is analyzed with the Petrimetrics probe
Quantify surface area per volume of gut smooth muscle layer with the Merz probe
Alzheimer’s researchers use the Area Fraction Fractionator Probe to find the percentage by volume of plaque in the cortex.
In this example, the Combined Point Intercept probe to quantify the area of the lumen and the boundary-length of the internal elastic lamina of the cross section of an artery.
By annotating 2D sections, create a data file that models the structures within your tissue that can be visualized in the interactive 3D environment where you can take high resolution screenshots or export movies for publications and presentations.
| Feature Description | ||||
|---|---|---|---|---|
| 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) |
Stereo Investigator is used across the globe by the most prestigious laboratories.
MBF Bioscience now offers customized models of Huron Digital Pathology’s TissueScope™, a line of whole slide scanners, and supports TissueScope images
Williston, VT – June 29, 2018 – MBF Bioscience is pleased to announce the launch of the Whole Slide Edition of
Stereo Investigator has been cited in over 8,000 published research papers. 5 times more than its nearest competitor.
Tang, F., L.-y. Zhou, et al.
Inhibition of ACSL4 Alleviates Parkinsonism Phenotypes by Reduction of Lipid Reactive Oxygen SpeciesView Publication
Sarangi, P., L. K. Pradhan, et al.
Di-2-ethylhexyl phthalate-induced neurobehavioural transformation is associated with altered glutathione biosynthesis and neurodegeneration in zebrafish brainView Publication
Jiang, W., Y. Cheng, et al.
Involvement of Abnormal p-α-syn Accumulation and TLR2-Mediated Inflammation of Schwann Cells in Enteric Autonomic Nerve Dysfunction of Parkinson’s Disease: an Animal Model StudyView Publication
Hua, F., H. Zhu, et al.
β-arrestin1 regulates astrocytic reactivity via Drp1-dependent mitochondrial fission: implications in postoperative deliriumView Publication
He, C.-B., Y. Jin, et al.
Collateral projections from the ventral tegmental area/substantia nigra pars compacta to the nucleus accumbens and insular cortex in the ratView Publication
Gullotta, G. S., D. De Feo, et al.
Age-induced alterations of granulopoiesis generate atypical neutrophils that aggravate stroke pathologyView Publication
The software will work with 2D whole slide images acquired from most slide scanners and research microscope imaging systems.
Researchers use Stereo Investigator Whole Slide Edition to perform quantitative analysis of cell populations, cell area and volume, fiber or capillary length, and area and volume of regions of interest.
Both programs allow researchers to obtain quantitative data from tissue specimens. However, Stereo Investigator can be used with live or acquired images and contains analyses for both thick and thin tissue specimens, while Stereo Investigator Whole Slide Edition has been tailored to accommodate 2D images of thin tissue and therefor only contains 2D stereological probes for thin tissue.
No. Stereo Investigator Whole Slide Edition contains 2D probes for thin tissue only. Optical Fractionator is a 3D probe for use with thick tissue and is available in MBF Bioscience’s original Stereo Investigator software.
"Our Stereo Investigator system works perfectly. We use it every day and don't have any problems whatsoever. Thanks for the good system."
"I have been using the Neurolucida and Stereo Investigator software from MicroBrightField for the last 5 years, and this software has become an essential part of my research program. Whether it is 3 dimensional reconstruction, counting particular particles or mapping the developing and adult vascular, these programs are a scientific must. I personally have been able to push my research in ways that would otherwise not have been possible. Furthermore, the ability to quantitate and detect subtle differences is and will continue to be critical to my scientific program. I would highly recommend these companion programs to any research scientist."
"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."
"We've used Stereo Investigator for 10+ years. The technical support is outstanding, and the company itself it highly responsive to their customers."
"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. "
"Stereo Investigator is a excellent stereology system. It is easy to work with and the workflows help you to work very efficiently. It is a crucial research tool for obtaining estimates of number of neurons, length of capillaires, length density of fibers, volume measurements of regions of interests or neurons, etc in specific brain regions. I would like to recommend it to everybody who is interested in stereology. In addition, MBF provides excellent technical support and helps you to find the best technical tools for your research challenges on morphometry."
"Stereo Investigator is an excellent research tool for unbiased stereology. In our research group when we set out to quantify the complex network nerves residing in the stomach mucosa. With Stereo Investigator we were able to get accurate estimates of numbers and show differences between your study groups without the introduction of sampling bias."
"Stereo Investigator has been the workhorse of our Microvascular Pathology Lab for the last six years. We have been able to measure vascular density with an accuracy never before available to our studies and more recently SI has provided efficient and precise comparisons of hypoxia and ischemic damage in cerebral vessels and neurons. The helpfulness, availability and experience of the MBF staff has been extraordinary. I would recommend any of their products wholeheartedly."
"Stereo Investigator is great for stereology. Although there is no field representation in the UK, the team in Vermont have been excellent at supporting us in our research applications. With online support and real time meetings and webinars, we've been able to make substantial progress on our research projects. MBF aren't afraid of a technical challenge, which is excellent, and have managed to provide us an excellent solution for our complex research needs."
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:
We offer a free expert demonstration of Stereo Investigator – Whole Slide 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.
The complete stereology solution. The gold standard for unbiased cell counting.
The gold standard in unbiased stereology for use on cleared tissue.
Automatic, accurate, unbiased, high-throughput cell quantification in histological specimens.