Stereo Investigator

Count cells and quantify lengths, areas, and volumes with the world's best and most-cited stereology system.

A Stereo Investigator system for stereology gives you accurate, unbiased estimates of the number, length, area, and volume of cells or biological structures in a tissue specimen. It is a key research tool that has helped lead advances in numerous areas of neuroscience including neurodegenerative diseases, neuropathy, memory, and behavior, as well as other research fields including pulmonary research, spinal cord research, and toxicology.


+ On our blog: How researchers used Stereo Investigator to discover that postnatal neurogenesis erases memories

In addition to stereology software, a Stereo Investigator system includes any hardware you need, such as a microscope, computer, motorized stage, camera, etc., and comes with MBF’s technical support for the entire system as well as research support to optimize your experimental design.

+ Watch a 5 minute video about Stereo Investigator:


Stereo Investigator has been cited in over 6,000 published research papers. 5 times more than its nearest competitor.

It has been used in breakthrough studies such as:

Akers, K. G., Martinez-Canabal, A., Restivo, L., Yiu, A. P., De Cristofaro, A., Hsiang, H.-L. L., . . . Shoji, H. (2014). Hippocampal Neurogenesis Regulates Forgetting During Adulthood and Infancy. Science, 344(6184), 598- 02.

Nagahara, A. H., D. A. Merrill, G. Coppola, S. Tsukada, B. E. Schroeder, G. M. Shaked, L. Wang, A. Blesch, A. Kim, J. M. Conner, E. Rockenstein, M. V. Chao, E. H. Koo, D. Geschwind, E. Masliah, A. A. Chiba and M. H. Tuszynski (2009). "Neuroprotective effects of brain-derived neurotrophic factor in rodent and primate models of Alzheimer's disease." Nature Medicine advanced online publication.

Santarelli, L., M. Saxe, C. Gross, A. Surget, F. Battaglia, S. Dulawa, N. Weisstaub, J. Lee, R. Duman, O. Arancio, C. Belzung and R. Hen (2003). "Requirement of Hippocampal Neurogenesis for the Behavioral Effects of Antidepressants." Science 301: 805-809.


Stereology on a microscope

Microscope hardware and Stereo Investigator software work in harmony to deliver a powerful, seamless stereology system. A typical system includes a microscope, computer, and Stereo Investigator software. Most of what is visible through the oculars is displayed on the computer screen. Add the Lucivid to Stereo Investigator and you can perform stereology while looking through the oculars.

Stereo Investigator fully integrates with your microscope and associated hardware to reduce manual work and to speed up data collection. It can:

  • direct motorized stages to automatically move for systematic random sampling of tissue specimen
  • control cameras so you can view live images or collect and save images and image stacks, even change or save camera settings for future use
  • control the focus position, change objective lenses or adjust the condenser
  • automatically change filter wheels and mirror cubes when acquiring fluorescent images or image stacks

Stereo Investigator works with brightfield, multi-channel fluorescence, confocal, structured illumination, and two-photon microscopes.  


Stereology from image stacks

Performing stereology at the microscope from fluorescent tissue specimens can be problematic since exposure to light degrades fluorescent tissue. With Stereo Investigator Desktop you can acquire image stacks using systematic random sampling (SRS) - a method that produces image stacks suitable for stereology- and then perform stereology on the image stacks. A great benefit of stereology on image stacks is that you can run many probes for different types of analyses and never have to worry that your tissue will fade. Plus, it's easier to double check the analysis.



During SRS image stack acquisition, Stereo Investigator directs the motorized stage, camera, and, for fluorescent images, the filter wheels and mirror cubes. This means you can automatically capture image stacks at each sample site, and then take the image stacks to a computer with Stereo Investigator Desktop and perform stereological analysis. Image stacks can be saved to Biolucida - a platform for viewing, sharing, and storing microscope images.

+ Read about how to analyze tissue cleared with CLARITY, SeeDB, 3DISCO, and more

Stereology on whole slide images

Whole slide images (digital replicas of your specimen) are a permanent digital resource you can use over and over again for analysis and publication images. Stereo Investigator can quickly and easily create whole slide images of your entire specimen in 3D (x, y, and z) or 2D (x, y) with the addition of the 2D and 3D Slide Scanning modules. The system is fully integrated and works unattended, allowing you to focus on other projects. Stereo Investigator directs the motorized stage, camera, and, for fluorescent images, the filter wheels and mirror cubes so there is no need for manual intervention. 

Whole slide images give you the freedom to perform stereology on a computer away from the microscope, and also give you a permanent digital file of your specimen that can be easily stored on Biolucida - a platform for viewing, sharing, and storing microscope images. Stereology on 2D whole slide images can be employed if the chosen probe does not require systematic random sampling, such as Cavalieri probe for regional area and volume, and Area Fraction Fractionator for calculating the area of a small subregion (such as lesions or plaques) within a larger region.

Stereo Investigator and Biolucida also work with whole slide images from providers such as Aperio and Nanozoomer. 

Customized stereology solutions

Stereo Investigator systems range from a cost-effective brightfield system up to a laser scanning confocal system.  We can integrate our software into microscopes and hardware that labs already own, or we can provide complete systems including microscopes, motorized stages, cameras, computers and software. Either way, our systems are fully integrated, allowing our software to drive motorized parts of the microscope system. Imaging modules and additional hardware can be added to your system as your needs evolve.


Each Stereo Investigator system we configure is:

●      Based upon your specific research needs.

●      Fully integrated - Stereo Investigator controls motorized stages, cameras, filter wheels etc.

●      Scalable, so it fits your budget and allows room for additional capabilities via our imaging modules and hardware upgrades.

●      Supported by our team of scientists and technicians who are experts in stereology, research software and laboratory hardware.  Our scientists also can help you design your study.

●      Upgradable to new software versions that are released regularly.

Stereo Investigator has been developed with support from the National Institute of Mental Health (NIMH)

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