In this paper, we present a novel method for analysis and segmentation of laminar structure of the cortex based on tissue characteristics whose change across the gray matter facilitates distinction between cortical layers. We develop and analyze features of individual neurons to investigate changes in architectonic differentiation and present a novel high-performance, automated tree-ensemble method trained on data manually labeled by three human investigators. From the location and basic measures of neurons, more complex features are developed and used in machine learning models for automatic segmentation of cortical layers. Tree ensembles are used on data manually labeled by three human experts. The most accurate classification results were obtained by training three models separately and creating another ensemble by combining probability outputs for final neuron layer classification. Measurement of importances of developed neuron features on both global model level and individual prediction level are obtained.
This is the second article in a series of three studies that investigate the anatomical determinants of thalamocortical (TC) input to excitatory neurons in a cortical column of rat primary somatosensory cortex (S1). Here, we report the number and distribution of NeuN-positive neurons within the C2, D2, and D3 TC projection columns in P27 rat somatosensory barrel cortex based on an exhaustive identification of 89834 somata in a 1.15 mm This chapter discusses the principles of classical architectonic mapping in the context of recent imaging techniques. It presents an observer-independent approach for a quantitative analysis of cortical areas and their borders, which is based on a multivariate statistical analysis of the cytoarchitecture and illustrates the application of this approach for the cytoarchitectonic mapping of the human visual cortex. Important criteria for cytoarchitectonic mapping are the absolute thickness of cortical layers, the proportionate thickness of a layer relative to the other cortical layers and to the total cortical depth, the presence of clearly recognizable laminar borders and vertical columns, the packing density and size of neuronal cell bodies, the homogeneous or clustered distribution of cell bodies throughout the layers, and the presence of special cell types such as Betz cells. Understanding the regional distributions of neurotransmitter receptors is likely to provide a crucial intermediary level of description between function and structure, since different cytoarchitectonic and functional areas have different mean receptor densities as well as distinct laminar distribution patterns. Another way for a better understanding of brain function and the underlying anatomy is to compare architectonic maps obtained in postmortem brains with activation maps obtained in functional imaging studies in a common spatial reference system. Since these two kinds of maps stem from different subsets of brains, such a comparison must be performed on a probabilistic basis.