Retinal topography maps in R: New tools for the analysis and visualization of spatial retinal data

B.A. Cohn, Shaun Collin, P.C. Wainwright, L. Schmitz

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

© 2015 ARVO. Retinal topography maps are a widely used tool in vision science, neuroscience, and visual ecology, providing an informative visualization of the spatial distribution of cell densities across the retinal hemisphere. Here, we introduce Retina, an R package for computational mapping, inspection of topographic model fits, and generation of average maps. Functions in Retina take cell count data obtained from retinal wholemounts using stereology software. Accurate visualizations and comparisons between different eyes have been difficult in the past, because of deformation and incisions of retinal wholemounts. We account for these issues by incorporation of the R package Retistruct, which results in a retrodeformation of the wholemount into a hemispherical shape, similar to the original eyecup. The maps are generated by thin plate splines, after the data were transformed into a two-dimensional space with an azimuthal equidistant plot projection. Retina users can compute retinal topography maps independent of stereology software choice and assess model fits with a variety of diagnostic plots. Functionality of Retina also includes species average maps, an essential feature for interspecific analyses. The Retina package will facilitate rigorous comparative studies in visual ecology by providing a robust quantitative approach to generate retinal topography maps.
Original languageEnglish
Pages (from-to)1-10
JournalJournal of Vision
Volume15
Issue number9
DOIs
Publication statusPublished - Jul 2015

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Spatial Analysis
Retina
Ecology
Software
Cell Count
Neurosciences
Spatial Navigation

Cite this

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Retinal topography maps in R: New tools for the analysis and visualization of spatial retinal data. / Cohn, B.A.; Collin, Shaun; Wainwright, P.C.; Schmitz, L.

In: Journal of Vision, Vol. 15, No. 9, 07.2015, p. 1-10.

Research output: Contribution to journalArticle

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AB - © 2015 ARVO. Retinal topography maps are a widely used tool in vision science, neuroscience, and visual ecology, providing an informative visualization of the spatial distribution of cell densities across the retinal hemisphere. Here, we introduce Retina, an R package for computational mapping, inspection of topographic model fits, and generation of average maps. Functions in Retina take cell count data obtained from retinal wholemounts using stereology software. Accurate visualizations and comparisons between different eyes have been difficult in the past, because of deformation and incisions of retinal wholemounts. We account for these issues by incorporation of the R package Retistruct, which results in a retrodeformation of the wholemount into a hemispherical shape, similar to the original eyecup. The maps are generated by thin plate splines, after the data were transformed into a two-dimensional space with an azimuthal equidistant plot projection. Retina users can compute retinal topography maps independent of stereology software choice and assess model fits with a variety of diagnostic plots. Functionality of Retina also includes species average maps, an essential feature for interspecific analyses. The Retina package will facilitate rigorous comparative studies in visual ecology by providing a robust quantitative approach to generate retinal topography maps.

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