Retistruct: A package to reconstruct flattened retinae
Frontiers in Neuroinformatics(2014)
Abstract
Event Abstract Back to Event Retistruct: A package to reconstruct flattened retinae David C Sterratt1*, Daniel Lyngholm2, David Willshaw1 and Ian D Thompson2 1 University of Edinburgh, UK 2 King’s College London, United Kingdom "In the course of studying the function and development of the visual system, cells in the retina are often labelled; for example, to determine the distribution of various types of cell in the retina, to assess the location of retrograde tracer or to measure the distribution of a guidance molecule. Following labelling the retina is dissected and flattened, and the distribution of labels is measured in the flattened retina. The dissection requires a number of incisions to be made and tears in the rim and incisions can develop. This complicates analysis as some cells that were close neighbours are now separated by the incisions. We present a computational method, implemented as an R package ("Retistruct"), that overcomes this problem by reconstructing the 3D shape of the retina so that the positions of the labels in the intact retina can be inferred. The input to the algorithm is the line segments of the flattened retinal outline, with incisions and tears marked up by an expert. The retinal outline is split into triangular elements whose positions are then transformed so that they lie on a partial sphere with the expected dimensions of the intact retina. The transformation is adjusted so as to minimise a physically-inspired deformation energy function. Our validation studies indicate that the algorithm is able to estimate the position of a point on the intact retina to within 8 degrees of arc. Once reconstructed, the retina can be visualised as a 3D object or on polar or sinusoidal projections onto the plane. By inversion and rotating of the optic axis, an estimate of the projection of the reconstructed retina into visual space can be obtained. A number of insights can be gained by using the method. (1) Because retinae are now described in a standard space, it allows for comparison of retrograde tracer experiments from a number of animals and the construction of composite anatomical maps. (2) The regions of the retinae that project onto the left or right dorsal lateral geniculate nucleus (dLGN) can be determined by injecting retrograde tracer into the dLGN (Coleman et al. 2009, Neuroscience 161:561-571; doi: http://dx.doi.org/10.1016/j.neuroscience.2009.03.045 ). Reconstruction allows regions of visual space that correspond to the monocular and binocular regions of the dLGN to be identified. (3) The correspondence between the density of S-opsin receptors and visual space can be measured." Keywords: General neuroinformatics, Visual Systems, Retina, 3D, computational model Conference: 5th INCF Congress of Neuroinformatics, Munich, Germany, 10 Sep - 12 Sep, 2012. Presentation Type: Demo Topic: Neuroinformatics Citation: Sterratt D, Lyngholm D, Willshaw D and Thompson I (2014). Retistruct: A package to reconstruct flattened retinae. Front. Neuroinform. Conference Abstract: 5th INCF Congress of Neuroinformatics. doi: 10.3389/conf.fninf.2014.08.00110 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: 21 Mar 2013; Published Online: 27 Feb 2014. * Correspondence: Dr. David C Sterratt, University of Edinburgh, Edinburgh, UK, david.c.sterratt@ed.ac.uk 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 David C Sterratt Daniel Lyngholm David Willshaw Ian D Thompson Google David C Sterratt Daniel Lyngholm David Willshaw Ian D Thompson Google Scholar David C Sterratt Daniel Lyngholm David Willshaw Ian D Thompson PubMed David C Sterratt Daniel Lyngholm David Willshaw Ian D Thompson 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.
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