Stereology Software

What is stereology? Unbiased stereology is now recognized in biological research as the best-practice method for quantitative histology. It is used to quantify the number of cells, the length of fibers, and the area and volume of regions. Stereology plays an important role in validating and rejecting experimental hypotheses in biological research. It produces results that are accurate, efficient, and more reliable than other ad hoc quantitative analyses. Unbiased stereology is often used to help answer questions such as:

  • Is the number of cells in a region of interest in experimental subjects different than controls?
  • Has the length of nerve fibers or blood vessels changed?
  • Has there been a change in volume of a region of interest?
  • How much of my region of interest has been damaged by an injury?

The field of stereology is broad. It can basically be divided into two underlying methodologies, unbiased stereology (also known as design based stereology) and all other stereological methods, which are biased. Unbiased stereology has been developed more recently.  It includes methods such as the Optical Fractionator, the Nucleator, and Space Balls. However, some older stereology methods continue to be used due to the lack of knowledge of the newer methods. For instance, counting cell profiles at the top of each physical section is a common practice that is biased and does not yield accurate results. 

This presentation contains more information about the theory of stereology

By using unbiased stereology, researchers get unbiased, accurate and reliable data. For this reason, many peer-reviewed journals require or recommend the use of unbiased stereology when quantifying cells or structures. The Stereo Investigator system for unbiased stereology has been cited in over 4,000 published papers, making it by far the most-cited unbiased stereology system in the world.

In order to obtain the accurate results that unbiased stereology is known for, it is important to follow certain practices, described in the literature, during tissue preparation. MBF has Ph.D. staff scientists who can give you practical support for all aspects of stereologic experimental design—from the tissue processing stage all the way to interpreting the results.

Additionally, MBF provides you with a host of expert stereological support that includes detailed software workflows within Stereo Investigator, extensive on-line documentation, videos and webinars. All of this is available to help guide you through the steps of a stereological study that are briefly outlined below.

1) Sample.  Systematic random sampling (SRS) is an unbiased and efficient way to select sample sites within the region of interest.  Stereo Investigator uses SRS to obtain a representative sample of the tissue.  The system first chooses a random starting site within the region of interest - a crucial step for SRS - then directs the motorized XY stage to automatically move at a constant interval to the subsequent sample sites.

2) Measure.  Cells or structures in the chosen sampling sites are counted or measured with probes – graphical shapes superimposed on the specimen. Stereo Investigator includes workflows for all of the most popular probes, along with detailed documentation that will guide you through any of the 30+ probes in the program. Stereo Investigator guides you to use the specific stereological rules to follow for each probe to ensure that you make accurate measurements.

3) Results.  The probe results are calculated to provide an accurate estimate of the counts or measurements for the region(s) of interest as a whole.  Stereo Investigator automatically calculates the results for you. The accuracy of the data is also calculated and provided as the coefficient of error. Stereo Investigator also exports results directly into Microsoft Excel so you can easily sort and further analyze the data.

+ Learn more about stereology
+ Learn more about Stereo Investigator
Read our book about stereology (with a focus on Neuroscience)

Expand your research capabilities with extension modules for Stereo Investigator

  • Virtual Tissue 2D - Create 2D whole slide images
  • Virtual Tissue 3D - Create 3D whole slide images
  • Image Stack and 3D Visualization - Acquire and view 3D image stacks suitable for stereology
  • Image Montaging - Automated 3D montaging/stitching of image stacks
  • MRI Support - Analyze MRI image sets
  • Serial Section Reconstruction - 3D anatomical reconstructions from serial section
  • Deconvolution - Deconvolution of brightfield, widefield fluorescence, and confocal images
  • Structured Illumination - Control of structured illumination hardware
  • Open Confocal - Unbiased cell counting/stereology on a confocal microscope
  • Zen Control - Unbiased cell counting/stereology on a Zeiss LSM confocal microscope
  • Fluoview - Unbiased cell counting/stereology on Olympus Fluoview 300 & 500

What to look for when purchasing a stereology system

  • Controls the microscope’s motorized stage and camera
  • Automatically changes filter wheels and mirror cubes for imaging fluorescent tissue
  • New versions of stereology software are released consistently
  • Research support is available
  • Supports the newest microscopes, motorized stages, and cameras
  • Offers technical support when moving or changing a stereology system
  • Built-in workflows for popular stereology probes
  • Thorough and helpful system manuals

In this webinar, Dr. Susan Hendricks answers questions about stereology theory, experimental design and Stereo Investigator software.