Population Structure Analysis of an Inbred Population using Quantitative Shape Phenotyping from Stereo Retinal Photographs

Li Tang; Michael D Abramoff

doi:10.48550/arxiv.2608.15471

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Population Structure Analysis of an Inbred Population using Quantitative Shape Phenotyping from Stereo Retinal Photographs

Preprint

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Population Structure Analysis of an Inbred Population using Quantitative Shape Phenotyping from Stereo Retinal Photographs

Li Tang and Michael D Abramoff

arXiv

08/16/2026

DOI: 10.48550/arxiv.2608.15471

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https://doi.org/10.48550/arxiv.2608.15471View

Preprint (Author's original) This preprint has not been evaluated by subject experts through peer review. Preprints may undergo extensive changes and/or become peer-reviewed journal articles. Open Access

Abstract

The population structure of an inbred population of 781 people on Norfolk Island in the Pacific, 318 of which are descendants of the original Mutineers of the Bounty, is analyzed phenotypically using shape from stereo retinal fundus photographs. Three-dimensional optic nerve head (ONH) shape is reconstructed from stereo pairs by a multi-scale stereo matching algorithm. Using deep neural network, the shape of ONH, which is under genetic control, is decomposed into a set of hierarchical features through self-taught learning. Features captured at different levels are selected according to their discriminant power in identifying the two populations. The prediction accuracy is evaluated with stratified cross validation. Given the selected feature set, individuals are grouped into k hierarchical clusters and cluster membership fractions are determined for k=2,3,4,5,6,7. Population structure analysis on the basis of phenotypes through image analysis allows heritability and linkage analysis, including founder effects from English and Polynesian ancestors, potentially leading to new genetic risk factors for glaucoma and other ONH-related eye diseases.

Computer Science - Computer Vision and Pattern Recognition

Computer Science - Learning

Quantitative Biology - Quantitative Methods

Details

Title: Subtitle: Population Structure Analysis of an Inbred Population using Quantitative Shape Phenotyping from Stereo Retinal Photographs
Creators: Li Tang - University of Iowa
Michael D Abramoff - University of Iowa
Resource Type: Preprint
Publication Details: arXiv
DOI: 10.48550/arxiv.2608.15471
ISSN: 2331-8422
Publisher: arXiv
Language: English
Date posted: 08/16/2026
Academic Unit: Electrical and Computer Engineering; Fraternal Order of Eagles Diabetes Research Center; Ophthalmology and Visual Sciences
Record Identifier: 9985219041602771

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