Swarm-Optimized Explainable Attention–Transformer Networks for Bacterial Colony Segmentation and Quantification

For microbiological diagnostics, accurately counting and segmenting microbial colonies is extremely important. However, manual methods are labor-intensive and yield inconsistent results. We develop a hybrid model using swarm intelligence, combining a convolutional transformer with nested skip connections and global context with channel and spatial attention. Parameter tuning is supported by a variety of swarm optimization algorithms (e.g., Particle Swarm Optimization, Quantum-behaved Particle Swarm Optimization, and Differential Evolution Particle Swarm Optimization). Morphological refinement, including a further watershed transform, an attention graph, and post-processing, enhances colony boundaries by separating them. Grad-CAM++, Integrated Gradients, and temperature scaling provide a transparent and trustworthy model through explainability and post hoc calibration. The proposed model was extensively tested on the Microbial Colony Recognition and Circular Bacterial Colony Datasets, achieving a Dice score of 94.2%, an Intersection over the Union of 88.6%, and a mean absolute counting error of 2.7 colonies. These results significantly outperform several baseline models, including U-Net (88.1%), U-Net++ (89.7%), Attention U-Net (90.6%), and Swin-Unet (91.4%). Statistically significant improvements were confirmed (p < 0.01). A cross-dataset analysis demonstrates the framework’s robustness and cross-domain applicability, and positions it as a trustworthy, explainable automated model for assessing microbial colonies in laboratory and clinical settings.