Axonal and dendritic density field estimation from incomplete single-slice neuronal reconstructions

Abstract

Event Abstract Back to Event Axonal and dendritic density field estimation from incomplete single-slice neuronal reconstructions Jaap Van Pelt1*, Arjen Van Ooyen1 and Harry B. Uylings2 1 VU University Amsterdam - Neuroscience Campus Amsterdam, Department of Integrative Neurophysiology - Center for Neurogenomics and Cognitive Research (CNCR), Netherlands 2 VU University Medical Center, Department of Anatomy & Neuroscience, Netherlands Neuronal signal integration and information processing in cortical networks critically depend on the organization of synaptic connectivity. Synaptic connections between neurons can form when their axons and dendrites come in close proximity of each other. The spatial innervation of neuronal arborizations can also be described by their axonal and dendritic mass density fields. Recently we showed that population mean density fields, averaged over a number of neurons of a given cell type, can be used for estimating synaptic connectivity between neurons with overlapping axonal and dendritic density fields (Van Pelt et al., 2010; Van Pelt and Van Ooyen, 2013). Deriving population mean density fields requires a sufficient number of experimentally reconstructed neurons. Much morphological data, made available via open-access databases, however, is derived from single slice neuronal reconstructions, which are generally incomplete because of cut branches. Here, we describe a method to recover the lost mass, which is based on an estimation of the mass inside the slices and an extrapolation of the mass to the space outside the slices, assuming axial symmetry in the spatial distribution of neuronal mass. This 'completion method' has been validated using a set of neurons generated with our NETMORPH simulator. These neurons were artificially sliced and subsequently recovered by the completion method. Dependent on the slice thickness and the extent of the arbors orphan branches may occur (inside branches which have lost their outside parents), which are not anymore part of the contiguous structure of the sliced neuron. For 300 micron thick slices, however, the validation showed a full recovery of dendritic mass and an almost full recovery of axonal mass. The completion method has been applied to three experimental data sets of reconstructed rat L2/3 pyramidal neurons. The recovery results showed that in 300 micron thick slices intracortical axons have lost by slicing about 50% of their mass and dendrites about 16% of their mass. The completion method can be applied to single slice reconstructions as long as axial symmetry can be assumed in the axonal and dendritic mass distribution. This opens the possibility to use the many cell-type specific reconstructions from open-access data bases for constructing, by completion, their population mean mass density fields and apply these fields in connectivity studies. References Van Pelt, J., Carnell, A., De Ridder, S., Mansvelder, H.D., and Van Ooyen, A. (2010). An algorithm for finding candidate synaptic sites in computer generated networks of neurons with realistic morphologies. Front. Comput. Neurosci., doi:10.3389/fncom.2010.00148. Van Pelt, J., and Van Ooyen, A. (2013). Estimating neuronal connectivity from axonal and dendritic density fields. Front. Comput. Neurosci. 7:160. doi:10.3389/ fncom.2013.00160. Keywords: reconstruction, slices, density fields, cut branches, Recovery Conference: Neuroinformatics 2014, Leiden, Netherlands, 25 Aug - 27 Aug, 2014. Presentation Type: Poster, not to be considered for oral presentation Topic: Computational neuroscience Citation: Van Pelt J, Van Ooyen A and Uylings HB (2014). Axonal and dendritic density field estimation from incomplete single-slice neuronal reconstructions. Front. Neuroinform. Conference Abstract: Neuroinformatics 2014. doi: 10.3389/conf.fninf.2014.18.00033 Copyright: The abstracts in this collection have not been subject to any Frontiers peer review or checks, and are not endorsed by Frontiers. They are made available through the Frontiers publishing platform as a service to conference organizers and presenters. The copyright in the individual abstracts is owned by the author of each abstract or his/her employer unless otherwise stated. Each abstract, as well as the collection of abstracts, are published under a Creative Commons CC-BY 4.0 (attribution) licence (https://creativecommons.org/licenses/by/4.0/) and may thus be reproduced, translated, adapted and be the subject of derivative works provided the authors and Frontiers are attributed. For Frontiers’ terms and conditions please see https://www.frontiersin.org/legal/terms-and-conditions. Received: 09 Apr 2014; Published Online: 04 Jun 2014. * Correspondence: Dr. Jaap Van Pelt, VU University Amsterdam - Neuroscience Campus Amsterdam, Department of Integrative Neurophysiology - Center for Neurogenomics and Cognitive Research (CNCR), Amsterdam, 1081 HV, Netherlands, jaapvanpelt46@gmail.com Login Required This action requires you to be registered with Frontiers and logged in. To register or login click here. Abstract Info Abstract The Authors in Frontiers Jaap Van Pelt Arjen Van Ooyen Harry B Uylings Google Jaap Van Pelt Arjen Van Ooyen Harry B Uylings Google Scholar Jaap Van Pelt Arjen Van Ooyen Harry B Uylings PubMed Jaap Van Pelt Arjen Van Ooyen Harry B Uylings Related Article in Frontiers Google Scholar PubMed Abstract Close Back to top Javascript is disabled. Please enable Javascript in your browser settings in order to see all the content on this page.