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J Neurosci Methods. 2012 Jun 15;207(2):181-8. doi: 10.1016/j.jneumeth.2012.04.010. Epub 2012 Apr 21.

Assessment of CA1 injury after global ischemia using supervised 2D analyses of nuclear pyknosis.

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Department of Pediatrics, University of Rochester Medical Center, Rochester, NY 14642, USA.


Selective neuronal vulnerability is a common theme in both acute and chronic diseases affecting the nervous system. This phenomenon is particularly conspicuous after global cerebral ischemia wherein CA1 pyramidal neurons undergo delayed death while surrounding hippocampal regions are relatively spared. While injury in this model can be easily demonstrated using either histological or immunological stains, current methods used to assess the cellular injury present in these biological images lack the precision required to adequately compare treatment effects. To address this shortcoming, we devised a supervised work-flow that can be used to quantify ischemia-induced nuclear condensation using microscopic images. And while we demonstrate the utility of this technique using models of ischemic brain injury, the approach can be readily applied to other paradigms in which programmed cell death is a major component.

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