Shrimp diseases continue to cause devastating losses in the aquaculture industry, driving a critical need for robust, automated detection. This work contributes the first application of Vision Transformers (ViT) and Self-Supervised Learning (SSL) to the shrimp farming domain, addressing both performance bottlenecks and data labeling challenges. We propose two deep learning pipelines to classify four key diseases: Healthy, Black Gill (BG), White Spot Syndrome Virus (WSSV), and a co-infection of both using a dataset of 4,348 images. First, our supervised transfer-learning approach leverages ImageNet-pretrained ViT-Small/16 and EfficientNet backbones. Second, we introduce a contrastive learning framework (SimCLR) with a ViT-Small encoder to extract robust representations from unlabeled images prior to fine-tuning. Our results establish strong new baselines for sustainable aquaculture monitoring. The supervised approach achieves an outstanding 96% accuracy with fast convergence, outperforming traditional generic models, while the label-efficient SSL approach reaches a highly competitive 85% validation accuracy.

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