Deep neural networks in medical microbiology for bacterial colonies classification

While automation has transformed many areas inside clinical laboratories, microbiology still relies heavily on manual tasks, particularly the culture of samples on agar plates and their subsequent manual review for microorganism identification and antibiotic susceptibility profiling. Bacterial colony detection and classification require trained professionals, making the process time-consuming and prone to human error. Developing deep learning models to automate these tasks could improve microbiology workflows and accelerate clinical decision-making. In this study we trained and evaluated five object detection architectures (Faster R-CNN and RetinaNet with ResNet-50 and ResNet-101 backbones, and YOLOv8) on the Annotated Germs for Automated Recognition (AGAR) dataset for bacterial colony classification. Transfer learning, cross-subset generalization, and Weighted Box Fusion (WBF) ensemble methods were applied to enhance and characterize performance. Additionally, we created and publicly released a curated dataset of 165 agar plate images containing colonies of S. aureus, P. aeruginosa, and E. coli cultured across four distinct culture media. YOLOv8m achieved a mean Average Precision (mAP) of 69.0% on the AGAR dataset, outperforming the best Detectron2 model (Faster R-CNN ResNet-101, 63.1%) by 5.9 percentage points. A four-model WBF ensemble combining both architectures reached 70.5% mAP (95% CI: 68.4-71.7). Cross-subset evaluation showed that a single model trained on the full dataset generalizes well to individual imaging conditions, making subset-specific fine-tuning largely unnecessary. On the curated dataset, a mixed ensemble reached 58.7% mAP (95% CI: 57.1-63.7). These results demonstrate that architecture choice and training data diversity are the primary drivers of performance for colony detection on agar plates.