Semi-automated quantification and neuroanatomical mapping of heterogeneous cell populations

Oscar A. Mendez, Colin J. Potter, Michael Valdez, Thomas Bello, Theodore P. Trouard, Anita A. Koshy

Research output: Contribution to journalArticlepeer-review

4 Scopus citations


Background: Our group studies the interactions between cells of the brain and the neurotropic parasite Toxoplasma gondii. Using an in vivo system that allows us to permanently mark and identify brain cells injected with Toxoplasma protein, we have identified that Toxoplasma-injected neurons (TINs) are heterogeneously distributed throughout the brain. Unfortunately, standard methods to quantify and map heterogeneous cell populations onto a reference brain atlas are time consuming and prone to user bias. New method: We developed a novel MATLAB-based semi-automated quantification and mapping program to allow the rapid and consistent mapping of heterogeneously distributed cells on to the Allen Institute Mouse Brain Atlas. The system uses two-threshold background subtraction to identify and quantify cells of interest. Results: We demonstrate that we reliably quantify and neuroanatomically localize TINs with low intra- or inter-observer variability. In a follow up experiment, we show that specific regions of the mouse brain are enriched with TINs. Comparison with existing methods: The procedure we use takes advantage of simple immunohistochemistry labeling techniques, use of a standard microscope with a motorized stage, and low cost computing that can be readily obtained at a research institute. To our knowledge there is no other program that uses such readily available techniques and equipment for mapping heterogeneous populations of cells across the whole mouse brain. Conclusion: The quantification method described here allows reliable visualization, quantification, and mapping of heterogeneous cell populations in immunolabeled sections across whole mouse brains.

Original languageEnglish (US)
Pages (from-to)98-104
Number of pages7
JournalJournal of Neuroscience Methods
StatePublished - Jul 15 2018


  • Atlas
  • Cell-mapping
  • Image processing
  • Semi-automated quantification
  • Toxoplasma gondii

ASJC Scopus subject areas

  • Neuroscience(all)


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