Stereo Investigator Software Update: Version 2024.1.3
We are pleased to announce the release of Stereo Investigator®version 2024.1.3, which introduces key updates to offline software licensing.
Stereo Investigator®
The complete stereology solution. The world’s most widely cited system for unbiased cell countingProduct 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.
Key Benefits
- Work with a trusted, reliable scientific tool that has over 8,000 citations
- Perform accurate, unbiased quantification of cells, fibers, capillaries, and any large or small biological structures
- Work directly on a microscope or acquire images for off-line analysis
- Use software workflows that simplify the use of complex stereological probes
- Cover all your research microscopy needs, including brightfield, darkfield and fluorescence microscopy using one of our flexible systems
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 11, 64-bit |
| Processor | 4-core |
| CPU RAM | 16 GB |
| GPU RAM | >6 GB |
| Recommended System Requirements | |
| Operating System | Windows 11, 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 |
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| * 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 | ||
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Computer controlled microscopes | Leica supported microscopes:
| Zeiss supported microscopes:
Nikon supported microscopes
Olympus BX and IX Series:
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| Manual microscopes | Most models after 2002 of Zeiss, Olympus, Nikon, Leica | |
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Structured illumination |
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| Filter wheels and shutters | Zeiss, Olympus, Leica, Nikon, LEP, Prior, Sutter | |
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Color video cameras |
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Monochrome video cameras |
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| Light sources |
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Supported Image File Formats: PDF
Contact us for an up-to-date list or question about specific models
Download Stereo Investigator brochure here.
Stereo Investigator® Version 2026.1.1
Released February 2026
New Features and Enhancements
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- Integration of stereologic probes tailored to large image volumes from cleared tissue, such as those acquired with the MBF Bioscience SLICE microscope
- Image Volume Fractionator for number/population estimates
- Image Volume SpaceBalls for fiber length estimates
- New Background Subtraction and Flat Field Correction image filters added to Slide Scanning and image compilation
- New Blending function in the Slide Scanning workflow
- New Tone Mapping image filter in the batch process pipeline helps reveal details in both bright and dim image regions
- Image support for .czi format has been improved
- Automatic stitching of overlapping fields of view in the Montage tool is now available
- Improvements to the movie creation tool:
- Generate movies at high resolution for large data sets
- Use image slice and partial projection views during movies to showcase image features
- Simple drag and drop to open .xml movie files
- Display the 3D scale bar while recording a Movie
- Additional general improvements and updates
- Improvements to the 2D scalebar options and placement
- AutoMove will now reposition focus when Continuous tracing is being used
- Image file paths are displayed in the Image Organizer
- Improved the image-handling capabilities for Measure Intensity channel options
View Full Version History Here.
Stereo Investigator: Key Features
Optical Fractionator Workflow
The Optical Fractionator probe is often the most appropriate stereological tool for counting the number of cells (or other objects) within a 3D region of interest. It yields accurate, quantitative data using reliable, proven methodology. This seemingly basic knowledge about a specimen can be immensely important, for example, helping researchers determine whether an experimental treatment affects the total number of cells within a brain region when compared to an untreated group.
Stereo Investigator provides the Optical Fractionator workflow which offers an easy-to-use, easy-to-learn interface that walks users through the complex process of correctly using the Optical Fractionator probe. New lab members can learn the process and be up and running quickly, while avoiding counting mistakes. This probe relies on systematic random sampling to obtain a statistically valid and unbiased sample of the region of interest. Stereo Investigator overlays a 3D disector (as appropriate for the specimen) that indicates where in the specimen to count cells using the probe. Once counting is complete, results are automatically calculated and can be viewed within the software, exported to Excel, or copied to the clipboard.
Stereo Investigator: Key Features
Wide Variety of Unbiased Estimators
In addition to the widely used Optical Fractionator probe, Stereo Investigator includes over 20 other stereological probes and estimators to evaluate numbers of objects, length, surface area, or volume/area of regions of interest. If you are looking for morphometric data in your research, Stereo Investigator can help you collect it in a way that is unbiased and repeatable.
Some examples include estimating:
- Cell population counts with the Optical Fractionator probe
- Length of capillaries using the Spaceballs probe
- Surface area with the Merz probe
- Regional volume/area utilizing the Cavalieri estimator
- Cell volume with the Nucleator probe
Stereo Investigator: Key Features
Stereology from SRS Image Stacks
For fluorescence microscopy, where minimizing light exposure is typically a concern, you can conduct stereological analyses on acquired images, rather than on a live microscope-camera feed. If desired, Stereo Investigator can help you save time on the microscope and space on image-storage devices by acquiring images from a representative portion of your specimen using systematic random sampling (SRS). Once you’ve acquired a set of statistically representative image-stacks, you can run many stereology probes for different types of morphometric analyses and never have to worry that your fluorescence signal will fade. In addition, you can repeat analyses easily if desired.
For SRS image/image-stack acquisition, Stereo Investigator directs the motorized stage, camera, and light sources. You can configure image-acquisition parameters, then let Stereo Investigator automatically capture image stacks at each SRS site. Perform stereological analysis on the acquired images using Stereo Investigator installed either on the microscope-control computer or on a different computer with the Desktop version of Stereo Investigator software.
Our Range of Stereology Solutions
| Feature Description | Stereo Investigator MICROSCOPE EDITION | Stereo Investigator DESKTOP 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) |
Case Studies
Inflammatory Loss of Lower Motor Neurons in Multiple Sclerosis
Vogt J, Paul F, Aktas O, Müller-Wielsch K, Dörr J, Dörr S, Bharathi BS, Glumm R, Schmitz C, Steinbusch H, Raine CS, Tsokos M, Nitsch R, Zipp F.
Multiple sclerosis involves substantial loss of lower motor neurons, not just demyelination. This study identifies immune-mediated, TRAIL-dependent neurodegeneration as a key mechanism.
Immune Cell Infiltration Distinguishes PSP from Other Parkinsonian Disorders
Couto B, Forrest SL, Fearon C, Lee S, Knott S, Li J, Fox SH, Tartaglia MC, Lang AE, Kovacs GG.
Progressive supranuclear palsy shows unexpected cytotoxic T-cell infiltration in the midbrain. This immune signature distinguishes PSP from Parkinson’s disease and control brains.
Design-Based Stereology Reveals Motoneuron Preservation Following VEGF Infusion
Storkebaum, E., Lambrechts, D., Dewerchin, M. et al.
Continuous delivery of VEGF provides robust neuroprotection in rat models of ALS. Motoneuron survival, neuromuscular connectivity, and lifespan are significantly preserved.
Blocking a Cell-Cycle Pathway to Protect Neurons After Spinal Cord Injury
Wu J, Kharebava G, Piao C, Stoica BA, Dinizo M, Sabirzhanov B, Hanscom M, Guanciale K, Faden AI.
Neuronal apoptosis after spinal cord injury is driven in part by E2F1/CDK1 signaling. Inhibiting this pathway significantly reduces neuronal loss and promotes neuroprotection.
Post-Stroke Exercise Enhances Axon Regeneration of Newborn Projection Neurons
Zhang QW, Deng XX, Sun X, Xu JX, Sun FY.
Physical exercise enhances neural repair after ischemic stroke. This study shows that treadmill training promotes axon regeneration of newborn projection neurons and improves motor recovery.
Unbiased Quantification of Synaptic Inputs Onto Single Neurons
Henny P, Brown MT, Micklem BR, Magill PJ, Bolam JP.
Using integrated light and electron microscopy, this work provides precise estimates of synapse number and distribution on single neurons. The approach enables quantitative links between neuronal structure and function.
Nuclear Hypertrophy Distinguishes Resilient Neurons in Asymptomatic Alzheimer’s Disease
Riudavets MA, Iacono D, Resnick SM, O'Brien R, Zonderman AB, Martin LJ, Rudow G, Pletnikova O, Troncoso JC.
Some individuals remain cognitively normal despite significant Alzheimer’s pathology. This study identifies distinctive neuronal structural features that may underlie resilience to neurodegeneration.
Comparing Alzheimer’s Mouse Models Through Quantitative Amyloid Plaque Mapping
Liu P, Reichl JH, Rao ER, McNellis BM, Huang ES, Hemmy LS, Forster CL, Kuskowski MA, Borchelt DR, Vassar R, Ashe KH, Zahs KR.
Amyloid plaque accumulation varies dramatically across commonly used AβPP transgenic mouse models. This quantitative comparison reveals large differences in plaque timing, burden, and regional distribution.
Quantitative Microvascular Analysis of Subcortical Regions in Schizophrenia
Kreczmanski P, Heinsen H, Mantua V, Woltersdorf F, Masson T, Ulfig N, Schmidt-Kastner R, Korr H, Steinbusch HW, Hof PR, Schmitz C.
Structural vascular alterations have been proposed as contributors to schizophrenia, yet direct anatomical evidence remains limited. Using unbiased stereological methods, this study examined whether microvessel architecture is altered in key subcortical regions of the human brain.
Neuron-Driven Vascular Degeneration in Familial Alzheimer’s Disease
Gama Sosa MA, Gasperi RD, Rocher AB, Wang AC, Janssen WG, Flores T, Perez GM, Schmeidler J, Dickstein DL, Hof PR, Elder GA.
Presenilin-1 familial Alzheimer’s disease mutations cause progressive microvascular degeneration in the hippocampus. These vascular defects arise independently of amyloid plaque deposition.
From Isolation to Impairment: Hippocampal Plasticity Changes in Adult Females
Pereda-Pérez I, Popović N, Otalora BB, Popović M, Madrid JA, Rol MA, Venero C.
Prolonged social isolation selectively impairs hippocampus-dependent contextual fear memory. This effect is associated with CA1 shrinkage and reduced synaptic PSA-NCAM expression.
Building Dopamine Neurons for Therapy: Stem Cell Grafts Restore Motor Function
Kriks, S., Shim, JW., Piao, J. et al.
Floor plate–derived human dopamine neurons show robust survival and functional integration after transplantation. This approach advances stem cell–based therapy for Parkinson’s disease.
Amyloid Plaques Do Not Predict Neuronal Loss in an Alzheimer’s Disease Model
Schmitz, Christoph et al
Hippocampal neuron loss occurs in APP/PS-1 transgenic mice independent of local amyloid plaque burden. These findings indicate that non–plaque-related mechanisms contribute to neurodegeneration in Alzheimer’s disease.
Selective Neuron Loss in the Dorsal Prefrontal Cortex During Normal Aging
Stranahan AM, Jiam NT, Spiegel AM, Gallagher M.
Aging leads to significant loss of both principal neurons and inhibitory interneurons in the dorsal prefrontal cortex. In contrast, ventral prefrontal regions remain structurally preserved.
Age-Related Cognitive Decline Occurs Without Hippocampal Neuron Loss
Rapp PR, Gallagher M.
Unbiased stereological analysis reveals no neuron loss in hippocampal subfields of aged rats with memory deficits.
Who Is Using Stereo Investigator?
Stereo Investigator is used across the globe by the most prestigious laboratories.
News and Updates
Unprecedented study reveals structure-function adaptations in the facial nucleus of elephants
Using specimens that were collected over three decades from zoos, researchers at Humboldt University of Berlin examined facial motor control in
INCF endorses the MBF Bioscience neuromorphological file format
We are pleased to announce that the International Neuroinformatics Coordinating Facility (INCF) has endorsed the MBF Bioscience neuromorphological file format as
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.
Rentsch, P., T. Egan, et al.
The ratio of M1 to M2 microglia in the striatum determines the severity of L-Dopa-induced dyskinesiasView Publication
González-Salvatierra, S., C. García-Fontana, et al.
Cardioprotective function of sclerostin by reducing calcium deposition, proliferation, and apoptosis in human vascular smooth muscle cellsView Publication
Bautista, J., M. Á. García-Cabezas, et al.
Pattern of ventral temporal lobe interconnections in rhesus macaquesView Publication
Wang, Z., D. Zheng, et al.
Enabling Survival of Transplanted Neural Precursor Cells in the Ischemic BrainView Publication
Villar-Conde, S., V. Astillero-Lopez, et al.
Synaptic involvement of the human amygdala in Parkinson’s diseaseView Publication
Stimpson, C. D., J. B. Smaers, et al.
Evolutionary scaling and cognitive correlates of primate frontal cortex microstructureView Publication
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
"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."
"Stereo Investigator was particularly useful for estimating cell density in larger brain structures, such as the inferior colliculus."
"Since we purchased our system four years ago, our experience with the MBF equipment and especially the MBF people has been outstanding. I cannot speak any higher about their professionalism and attention for our needs. "
"Stereo Investigator is powerful yet easy to use. The staff at MBF Bioscience is always helpful answering our questions and recommending optimal ways to conduct our stereological analyses."
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.
>> Learn More - Webinars
We’ve created over 55 webinars that demonstrate our products & their uses.
>> Learn More
Request More Information
We offer a free 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.
