A Systematic Multi-Dataset, Multi-Seed Evaluation of Preprocessing Strategies for Retinal Optic Disc and Cup Segmentation

Background/Objectives: Accurate delineation of the optic disc and optic cup in retinal fundus photographs is a prerequisite for automated glaucoma screening. While encoder–decoder segmentation models have advanced considerably, the contribution of upstream preprocessing to segmentation accuracy, and the stability of that contribution across repeated training runs, remain insufficiently characterized. Methods: Five preprocessing pipelines, baseline, Contrast Limited Adaptive Histogram Equalization (CLAHE), Region of Interest (ROI) cropping, ROI+CLAHE, and CLAHE with heavy augmentation, were benchmarked under a fixed EfficientUNet++ model with an EfficientNet-B7 encoder on three publicly available fundus datasets (REFUGE, ORIGA, and Drishti-GS). Every configuration was retrained under three independent random seeds (42, 15, and 89) to assess run-to-run variability. Seed-level standard deviations accompany every reported mean and define the confidence limit on each ranking. Results: On REFUGE, CLAHE with augmentation (Config 5) achieved the strongest mean Dice (disc 0.9523±0.0017; cup 0.8348±0.0018). On ORIGA, all five configurations clustered within 0.0067 disc Dice; ROI+CLAHE (Config 4) was marginally ahead on disc (0.9681±0.0002) and augmentation led on the cup (0.8873±0.0024). On Drishti-GS, all five configurations converged successfully once optimizer and loss settings were corrected; the near-total failures seen in earlier single-run experiments reflected a configuration problem, not the small (81-image) training set. Conclusions: CLAHE applied to full-resolution images is the single most consistently beneficial preprocessing choice across all three datasets. ROI+CLAHE showed a small, initialization-stable advantage on ORIGA, but ROI crop centres were derived from ground-truth centroids, an oracle localization setting, and these results should not be interpreted as achievable by a fully automated pipeline. Data augmentation showed a consistent reduction in initialization sensitivity on small datasets and may be beneficial as a default strategy.