A new method to represent and compute the 3-dimensional anatomy of fibrodendritic layers in the inferior colliculus

A method of graphically reconstructing and mathematically determining the three-dimensional orientation of the layered neurons in the inferior colliculus (IC) is introduced. A series of images is taken with a confocal microscope at discrete steps. These images are processed by an algorithm that emphasizes the closely spaced, layered dendrites within the central nucleus of the IC. The core of this approach lies in applying a combination of gradient (directional), median, and low-pass filters to extract contours of the lamina. The bit-mapped images are converted to vector lists, and the objects in a single layer are selected for linear regression analysis. A surface model that represents the layer is created by connecting the regression lines from each section. The spatial orientation of the surface is calculated as the vector cross product from each polygon in the surface. The average of all the normal vectors is taken to represent the orientation of the neural layer in 3-D space