Distribution of cells in mouse neocortex analysed with an open-source software utilising Ripley's K-function

The true revolution in the age of digital neuroanatomy is the ability to extensively quantify
anatomical structures and thus investigate structure-function relationship in great detail. To facilitate these efforts we have developed a MATLAB-based software that uses Ripley´s K-function to detect non-random patterns in the 3D distribution of cells. Genetically labelled layer 5 pyramidal neurons in somatosensory barrel cortex have been shown to be organized in a non-random order (Jafari-Mamaghani, Andersson, Krieger 2010). To investigate if there is a "canonical anatomical circuit" we have compared the distribution of genetically labeled layer 5 pyramidal neurons in barrel and visual cortex. Neocortex can be subdivided into 6 layers based on cell density and cell types. To investigate if in addition there are other organizational principles distinguishing the layers we analyzed the distribution of excitatory cells in the different layers.