MultiHeadGAN: A deep learning method for low contrast retinal pigment epithelium cell segmentation with fluorescent flatmount microscopy images
Year: 2022
Type: article
Abstract: BACKGROUND: Retinal pigment epithelium (RPE) aging is an important cause of vision loss. As RPE aging is accompanied by changes in cell morphological features, an accurate segmentation of RPE cells is a prerequisite to such morphology analyses. Due the overwhelmingly large cell number, manual annotations of RPE cell borders are time-consuming. Computer based methods do not work well on cells with weak or missing borders in the impaired RPE sheet regions. METHOD: To address such a challenge, we develop a semi-supervised deep learning approach, namely MultiHeadGAN, to segment low contrast cells from impaired regions in RPE flatmount images. The developed deep learning model has a multi-head structure that allows model training with only a small scale of human annotated data. To strengthen model learning, we further train our model with RPE cells without ground truth cell borders by generative adversarial networks. Additionally, we develop a new shape loss to guide the network to produce closed cell borders in the segmentation results. RESULTS: In this study, 155 annotated and 1,640 unlabeled image patches are included for model training. The testing dataset consists of 200 image patches presenting large impaired RPE regions. The average RPE segmentation performance of the developed model MultiHeadGAN is 85.4 (correct rate), 88.8 (weighted correct rate), 87.3 (precision), and 80.1 (recall), respectively. Compared with other state-of-the-art deep learning approaches, our method demonstrates its superior qualitative and quantitative performance. CONCLUSIONS: Suggested by our extensive experimental results, our developed deep learning method can accurately segment cells in RPE flatmount microscopy images and is promising to support large scale cell morphological analyses for RPE aging investigations.
Language: English
Topic: Retinal Imaging and Analysis
Subfield: Radiology, Nuclear Medicine and Imaging
Field: Medicine
Domain: Health Sciences
Open Access status: hybrid
Estimated APC paid: $2,300
Funders: National Science Foundation, U.S. Department of Veterans Affairs, Abraham J. and Phyllis Katz Foundation, Conselho Nacional de Desenvolvimento Científico e Tecnológico, Fundação de Amparo à Pesquisa do Estado de Minas Gerais, National Institutes of Health, National Eye Institute, National Cancer Institute, National Institute of General Medical Sciences
Awards: Predoctoral Training Program in Genetics, G1218959516, G2213472505, G2290346738, G2360859268, G2762772258, Computational pathology software for integrative cancer research with three-dimensional digital slides, Ocular Growth, Emmetropia, and Interphotoreceptor Retinoid-Binding Protein (IRBP), Exercise-induced Retinal Neuroprotection, G3544895813, G3590503360, G369404675, CAREER: High Performance Spatial Queries and Analytics for Spatial Big Data, CIF21 DIBBs: Middleware and High Performance Analytics Libraries for Scalable Data Science, G5395705277, G5924437800, The RPE and Recovery of the Blood Retina Barrier, G8866564872, G9000262189, P30-Core Grant for Vision Research, VIsion Science Training in Atlanta
OpenAlex ID: W4229457197