Towards Explainable Automated Neuroanatomy

Abstract: We present a novel method for quantifying the microscopic structure of brain tissue. It is based on the automated recognition of interpretable features obtained by analyzing the shapes of cells. This contrasts with prevailing methods of brain anatomical analysis in two ways. First, contemporary methods use gray-scale values derived from smoothed version of the anatomical images, which dissipated valuable information from the texture of the images. Second, contemporary analysis uses the output of black-box Convolutional Neural Networks, while our system makes decisions based on interpretable features obtained by analyzing the shapes of individual cells. An important benefit of this open-box approach is that the anatomist can understand and correct the decisions made by the computer. Our proposed system can accurately localize and identify existing brain structures. This can be used to align and coregistar brains and will facilitate connectomic studies for reverse engineering of brain circuitry.