biostudies-literatureValmaggia PSwiss National Science Foundation25https://www.ebi.ac.uk/biostudies/studies/S-EPMC9526362biostudies-literatureUnknown11(9)<h4>Purpose</h4>To evaluate the feasibility of automated segmentation of pigmented choroidal lesions (PCLs) in optical coherence tomography (OCT) data and compare the performance of different deep neural networks.<h4>Methods</h4>Swept-source OCT image volumes were annotated pixel-wise for PCLs and background. Three deep neural network architectures were applied to the data: the multi-dimensional gated recurrent units (MD-GRU), the V-Net, and the nnU-Net. The nnU-Net was used to compare the performance of two-dimensional (2D) versus three-dimensional (3D) predictions.<h4>Results</h4>A total of 121 OCT volumes were analyzed (100 normal and 21 PCLs). Automated PCL segmentations were successful with all neural networks. The 3D nnU-Net predictions showed the highest recall with a mean of 0.77 ± 0.22 (MD-GRU, 0.60 ± 0.31; V-Net, 0.61 ± 0.25). The 3D nnU-Net predicted PCLs with a Dice coefficient of 0.78 ± 0.13, outperforming MD-GRU (0.62 ± 0.23) and V-Net (0.59 ± 0.24). The smallest distance to the manual annotation was found using 3D nnU-Net with a mean maximum Hausdorff distance of 315 ± 172 µm (MD-GRU, 1542 ± 1169 µm; V-Net, 2408 ± 1060 µm). The 3D nnU-Net showed a superior performance compared with stacked 2D predictions.<h4>Conclusions</h4>The feasibility of automated deep learning segmentation of PCLs was demonstrated in OCT data. The neural network architecture had a relevant impact on PCL predictions.<h4>Translational relevance</h4>This work serves as proof of concept for segmentations of choroidal pathologies in volumetric OCT data; improvements are conceivable to meet clinical demands for the diagnosis, monitoring, and treatment evaluation of PCLs.Translational vision science & technologyFeasibility of Automated Segmentation of Pigmented Choroidal Lesions in OCT Data With Deep Learning.PMC9526362323530199395Hormann BKaiser PCattin PCMaloca PMSandkuhler RScholl HPNValmaggia PFriedli PfalseFeasibility of Automated Segmentation of Pigmented Choroidal Lesions in OCT Data With Deep Learning.<h4>Purpose</h4>To evaluate the feasibility of automated segmentation of pigmented choroidal lesions (PCLs) in optical coherence tomography (OCT) data and compare the performance of different deep neural networks.<h4>Methods</h4>Swept-source OCT image volumes were annotated pixel-wise for PCLs and background. Three deep neural network architectures were applied to the data: the multi-dimensional gated recurrent units (MD-GRU), the V-Net, and the nnU-Net. The nnU-Net was used to compare the performance of two-dimensional (2D) versus three-dimensional (3D) predictions.<h4>Results</h4>A total of 121 OCT volumes were analyzed (100 normal and 21 PCLs). Automated PCL segmentations were successful with all neural networks. The 3D nnU-Net predictions showed the highest recall with a mean of 0.77 ± 0.22 (MD-GRU, 0.60 ± 0.31; V-Net, 0.61 ± 0.25). The 3D nnU-Net predicted PCLs with a Dice coefficient of 0.78 ± 0.13, outperforming MD-GRU (0.62 ± 0.23) and V-Net (0.59 ± 0.24). The smallest distance to the manual annotation was found using 3D nnU-Net with a mean maximum Hausdorff distance of 315 ± 172 µm (MD-GRU, 1542 ± 1169 µm; V-Net, 2408 ± 1060 µm). The 3D nnU-Net showed a superior performance compared with stacked 2D predictions.<h4>Conclusions</h4>The feasibility of automated deep learning segmentation of PCLs was demonstrated in OCT data. The neural network architecture had a relevant impact on PCL predictions.<h4>Translational relevance</h4>This work serves as proof of concept for segmentations of choroidal pathologies in volumetric OCT data; improvements are conceivable to meet clinical demands for the diagnosis, monitoring, and treatment evaluation of PCLs.2022-01-01T00:00:00Z2022 Sep2026-06-01T02:10:26.779Z2025-02-19T01:28:33.49ZS-EPMC95263623615672910.1167/tvst.11.9.25