Cell and Tissue Research

, Volume 360, Issue 1, pp 29–42 | Cite as

How to count cells: the advantages and disadvantages of the isotropic fractionator compared with stereology

  • Suzana Herculano-HouzelEmail author
  • Christopher S. von Bartheld
  • Daniel J. Miller
  • Jon H. Kaas


The number of cells comprising biological structures represents fundamental information in basic anatomy, development, aging, drug tests, pathology and genetic manipulations. Obtaining unbiased estimates of cell numbers, however, was until recently possible only through stereological techniques, which require specific training, equipment, histological processing and appropriate sampling strategies applied to structures with a homogeneous distribution of cell bodies. An alternative, the isotropic fractionator (IF), became available in 2005 as a fast and inexpensive method that requires little training, no specific software and only a few materials before it can be used to quantify total numbers of neuronal and non-neuronal cells in a whole organ such as the brain or any dissectible regions thereof. This method entails transforming a highly anisotropic tissue into a homogeneous suspension of free-floating nuclei that can then be counted under the microscope or by flow cytometry and identified morphologically and immunocytochemically as neuronal or non-neuronal. We compare the advantages and disadvantages of each method and provide researchers with guidelines for choosing the best method for their particular needs. IF is as accurate as unbiased stereology and faster than stereological techniques, as it requires no elaborate histological processing or sampling paradigms, providing reliable estimates in a few days rather than many weeks. Tissue shrinkage is also not an issue, since the estimates provided are independent of tissue volume. The main disadvantage of IF, however, is that it necessarily destroys the tissue analyzed and thus provides no spatial information on the cellular composition of biological regions of interest.


Numbers of neurons Brain size Isotropic fractionator Stereology NeuN 



Thanks to Roberto Lent for supporting the creation of the isotropic fractionator, to Nicole Young and Christine Collins for establishing the automated variation and to Paul Manger for insights on tissue storage. Flow cytometry experiments were conducted in the Vanderbilt Medical Center Flow Cytometry Shared Resource and aided by the expertise of David K. Flaherty.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  • Suzana Herculano-Houzel
    • 1
    • 2
    Email author
  • Christopher S. von Bartheld
    • 3
  • Daniel J. Miller
    • 4
  • Jon H. Kaas
    • 4
  1. 1.Instituto de Ciências BiomédicasUniversidade Federal do Rio de JaneiroRio de JaneiroBrazil
  2. 2.Instituto Nacional de Neurociência TranslacionalMinistério de Ciência e TecnologiaSao PauloBrazil
  3. 3.Department of Physiology and Cell BiologyUniversity of Nevada School of MedicineRenoUSA
  4. 4.Department of PsychologyVanderbilt UniversityNashvilleUSA

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