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 4,000 published research papers.  

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

A typical Stereo Investigator system includes a computer connected to a microscope. Most of what is visible through the oculars is displayed on the computer screen. Stereo Investigator fully integrates with your microscope and associated hardware for quicker 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 on an offline workstation

Pair Stereo Investigator with the Image Stack extension module and you will be able to acquire SRS image stacks (image stacks suitable for stereology) so you can perform your stereological analysis on a workstation, freeing up valuable mircroscope time.  This also creates a permanent digital version of your slides that you can use over and over again, since unlike fluorescent tissue, digital images don't degrade, fade or bleach while you run probes or collect stereological data.

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 the workstation edition of Stereo Investigator and perform stereological analysis. Image stacks can be saved to the Biolucida Cloud for easy retrieval.

+ 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, and are easily stored in Biolucida Cloud and analyzed with Stereo Investigator.

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 Virtual Tissue 3D or 2D 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 Cloud, our image viewing, sharing, and storing software. Whole slide stereology can be employed if the chosen probe does not require systematic random sampling, such as Cavalieri 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 Cloud 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 that 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. Extension 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 extension 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.

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Stereo Investigator has been developed with support from SBIR grants awarded by the NIMH.