%A van Pelt,Jaap
%A van Ooyen,Arjen
%D 2013
%J Frontiers in Computational Neuroscience
%C
%F
%G English
%K Neuronal morphology,density fields,Synaptic connectivity,3D line crossing,random lines,intersections of cubes
%Q
%R 10.3389/fncom.2013.00160
%W
%L
%N 160
%M
%P
%7
%8 2013-November-25
%9 Methods
%+ Dr Jaap van Pelt,VU University Amsterdam - Neuroscience Campus Amsterdam,Department of Integrative Neurophysiology - Center for Neurogenomics and Cognitive Research (CNCR),De Boelelaan 1085,Amsterdam,1081 HV,Netherlands,jaapvanpelt46@gmail.com
%#
%! Connectivity estimation from density fields
%*
%<
%T Estimating neuronal connectivity from axonal and dendritic density fields
%U https://www.frontiersin.org/article/10.3389/fncom.2013.00160
%V 7
%0 JOURNAL ARTICLE
%@ 1662-5188
%X Neurons innervate space by extending axonal and dendritic arborizations. When axons and dendrites come in close proximity of each other, synapses between neurons can be formed. Neurons vary greatly in their morphologies and synaptic connections with other neurons. The size and shape of the arborizations determine the way neurons innervate space. A neuron may therefore be characterized by the spatial distribution of its axonal and dendritic “mass.” A population mean “mass” density field of a particular neuron type can be obtained by averaging over the individual variations in neuron geometries. Connectivity in terms of candidate synaptic contacts between neurons can be determined directly on the basis of their arborizations but also indirectly on the basis of their density fields. To decide when a candidate synapse can be formed, we previously developed a criterion defining that axonal and dendritic line pieces should cross in 3D and have an orthogonal distance less than a threshold value. In this paper, we developed new methodology for applying this criterion to density fields. We show that estimates of the number of contacts between neuron pairs calculated from their density fields are fully consistent with the number of contacts calculated from the actual arborizations. However, the estimation of the connection probability and the expected number of contacts per connection cannot be calculated directly from density fields, because density fields do not carry anymore the correlative structure in the spatial distribution of synaptic contacts. Alternatively, these two connectivity measures can be estimated from the expected number of contacts by using empirical mapping functions. The neurons used for the validation studies were generated by our neuron simulator NETMORPH. An example is given of the estimation of average connectivity and Euclidean pre- and postsynaptic distance distributions in a network of neurons represented by their population mean density fields.