arXiv:2611.13191v1 Announce Type: new Abstract: Background: Geographic atrophy (GA) is an advanced form of age-related macular degeneration (AMD). It causes irreversible vision loss due to progressive degeneration of the retinal pigment epithelium (RPE) and photoreceptors. Accurate segmentation of GA in en-face image is crucial for early diagnosis, monitoring disease progression, and developing personalized treatment strategies. However, existing deep learning approaches are typically evaluated using single architectures and single-device datasets, limiting insight into relative performance and cross-device robustness. Methods: We trained and systematically compared five deep learning architectures for GA segmentation: Nested U-Net, ResU-Net, nnUnet, Swin-Unet and MedSegDiff model, together with a thresholding based classical baseline. The models were trained on a dataset of en-face OCT images derived from 269 OCT volumes from two different devices, following a three-step preprocessing technique involving normalization and inpainting to enhance the quality of the en-face images. Results: On the fixed held-out validation set comprising OCT scans from both Cirrus (R) (Carl Zeiss Meditec, Inc., USA) and Spectralis (R) (Heidelberg Engineering, Germany) devices, nnUnet achieved the highest mean Dice similarity coefficient (DSC) of 0.8882 +/- 0.0033. The other models yielded the following Dice scores: Nested U-Net (0.7932 +/- 0.0423), ResU-Net (0.8453 +/- 0.0074), Swin-Unet (0.6886 +/- 0.0294), and Diffusion model (0.7959 +/- 0.0242). Conclusions: nnUnet framework, demonstrated most reliable performance for GA segmentation in en-face OCT under limited data conditions. It offers the best balance of accuracy, stability, and efficiency for GA quantification.