title: Analysis of spatial relationships in three dimensions: tools for the study of nerve cell patterning.
abstract: BACKGROUND
  Multiple technologies have been brought to bear on understanding the three-dimensional morphology of individual neurons and glia within the brain, but little progress has been made on understanding the rules controlling cellular patterning. We describe new matlab-based software tools, now available to the scientific community, permitting the calculation of spatial statistics associated with 3D point patterns. The analyses are largely derived from the Delaunay tessellation of the field, including the nearest neighbor and Voronoi domain analyses, and from the spatial autocorrelogram.
  
  
  RESULTS
  Our tools enable the analysis of the spatial relationship between neurons within the central nervous system in 3D, and permit the modeling of these fields based on lattice-like simulations, and on simulations of minimal-distance spacing rules. Here we demonstrate the utility of our analysis methods to discriminate between two different simulated neuronal populations.
  
  
  CONCLUSIONS
  Together, these tools can be used to reveal the presence of nerve cell patterning and to model its foundation, in turn informing on the potential developmental mechanisms that govern its establishment. Furthermore, in conjunction with analyses of dendritic morphology, they can be used to determine the degree of dendritic coverage within a volume of tissue exhibited by mature nerve cells.
authors.affiliation: Cambridge Computational Biology Institute, Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, CB3 0WA, UK. sje30@cam.ac.uk
authors.forename: Stephen J
authors.initials: SJ
authors.lastname: Eglen
authors.forename: Dan D
authors.initials: DD
authors.lastname: Lofgreen
authors.forename: Mary A
authors.initials: MA
authors.lastname: Raven
authors.forename: Benjamin E
authors.initials: BE
authors.lastname: Reese
mesh_terms: D000818:Animals; D016022:Case-Control Studies; D003952:Diagnostic Imaging / Q000379:methods; D006801:Humans; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D021621:Imaging, Three-Dimensional / Q000379:methods*; D009457:Neuroglia / Q000166:cytology / Q000502:physiology; D009474:Neurons / Q000166:cytology / Q000502:physiology*; D015203:Reproducibility of Results; D012984:Software