title: 3D segmentations of neuronal nuclei from confocal microscope image stacks.
abstract: In this paper, we present an algorithm to create 3D segmentations of neuronal cells from stacks of previously segmented 2D images. The idea behind this proposal is to provide a general method to reconstruct 3D structures from 2D stacks, regardless of how these 2D stacks have been obtained. The algorithm not only reuses the information obtained in the 2D segmentation, but also attempts to correct some typical mistakes made by the 2D segmentation algorithms (for example, under segmentation of tightly-coupled clusters of cells). We have tested our algorithm in a real scenario-the segmentation of the neuronal nuclei in different layers of the rat cerebral cortex. Several representative images from different layers of the cerebral cortex have been considered and several 2D segmentation algorithms have been compared. Furthermore, the algorithm has also been compared with the traditional 3D Watershed algorithm and the results obtained here show better performance in terms of correctly identified neuronal nuclei.
authors.affiliation: Department of Functional and Systems Neurobiology, Instituto Cajal (Consejo Superior de Investigaciones Científicas) Madrid, Spain.
authors.forename: Antonio
authors.initials: A
authors.lastname: Latorre
authors.affiliation: Department of Functional and Systems Neurobiology, Instituto Cajal (Consejo Superior de Investigaciones Científicas) Madrid, Spain ; Laboratorio Cajal de Circuitos Corticales, Centro de Tecnología Biomédica, Universidad Politécnica de Madrid Madrid, Spain.
authors.forename: Lidia
authors.initials: L
authors.lastname: Alonso-Nanclares
authors.affiliation: DATSI, Facultad de Informática, Universidad Politécnica de Madrid Madrid, Spain.
authors.forename: Santiago
authors.initials: S
authors.lastname: Muelas
authors.affiliation: DATSI, Facultad de Informática, Universidad Politécnica de Madrid Madrid, Spain.
authors.forename: José-María
authors.initials: JM
authors.lastname: Peña
authors.affiliation: Department of Functional and Systems Neurobiology, Instituto Cajal (Consejo Superior de Investigaciones Científicas) Madrid, Spain ; Laboratorio Cajal de Circuitos Corticales, Centro de Tecnología Biomédica, Universidad Politécnica de Madrid Madrid, Spain.
authors.forename: Javier
authors.initials: J
authors.lastname: Defelipe
keywords: 3D reconstruction; automatic segmentation; cerebral cortex; image processing; neuron