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Deep Learning Based Classification of UTI Pathogens on Agar Plate Images Using YOLO11 and EfficientNetV2-M


Authors : Dr. Arpitha C. N.; Sahana V. S.; Dr. Pushpa Ravikumar; Dr. Anser Pasha C. A.

Volume/Issue : Volume 11 - 2026, Issue 6 - June


Google Scholar : https://tinyurl.com/4xbxf8fa

Scribd : https://tinyurl.com/3jx9knfa

DOI : https://doi.org/10.38124/ijisrt/26jun1678

Note : A published paper may take 4-5 working days from the publication date to appear in PlumX Metrics, Semantic Scholar, and ResearchGate.


Abstract : This paper presents a two-stage deep learning pipeline for automated classification of urinary tract infection (UTI) pathogens from agar plate images. Stage 1 employs YOLO11m for colony detection on full annotated agar plate images from three public datasets. Stage 2 employs EfficientNetV2-M with a custom classifier head (1280→512→5) identifying five clinically significant UTI pathogens: Escherichia coli, Klebsiella pneumoniae, Proteus mirabilis, Pseudomonas aeruginosa, and Staphylococcus aureus.

Keywords : UTI Pathogen Classification; YOLO11; EfficientNetV2-M; Agar Plate Analysis; Bacterial Colony Detection; CLAHE.

References :

  1. Flores-Mireles, A., Walker, J., Caparon, M. et al. Urinary tract infections: epidemiology, mechanisms of infection and treatment options. Nat Rev Microbiol 13, 269–284 (2015). https://doi.org/10.1038/nrmicro3432
  2. Zuraszek, M. et al., "AGAR: A microbial colony dataset for deep learning detection," Scientific Data, vol. 10, 2021. arXiv:2108.01234
  3. Zieliński B, Plichta A, Misztal K, Spurek P, Brzychczy-Włoch M, Ochońska D (2017) Deep learning approach to bacterial colony classification. PLoS ONE 12(9): e0184554. https://doi.org/10.1371/journal.pone.0184554.
  4. Sunanda, I. B K, D. V, D. S. K and G. C. Sai Manusha, "Classification of Bacteria from Agar Plate Using Deep Learning and Image Processing," 2024 International Conference on Advances in Data Engineering and Intelligent Computing Systems (ADICS), Chennai, India, 2024, pp. 1-6, doi: 10.1109/ADICS58448.2024.10533650..
  5. M. Kutbi et al., "Leveraging Smartphone Imaging and Deep Transfer Learning for Bacterial Colony Classification: From Uncontrolled to Controlled Settings," in IEEE Access, vol. 13, pp. 184694-184708, 2025, doi: 10.1109/ACCESS.2025.3625648.
  6. Tan, M. and Le, Q., "EfficientNetV2: Smaller models and faster training," in Proc. ICML, 2021, pp. 10096–10106. arXiv:2104.00298
  7. Raghu, M. et al., "Transfusion: Understanding transfer learning for medical imaging," in NeurIPS, 2019, pp. 3347–3357. arXiv:1902.07208
  8. Makrai, L., Fodróczy, B., Nagy, S.Á. et al. Annotated dataset for deep-learning-based bacterial colony detection. Sci Data 10, 497 (2023). https://doi.org/10.1038/s41597-023-02404-8.
  9. Du, J. (2026). Clinical Dataset of 19 Bacterial Colony Images. Zenodo. https://doi.org/10.5281/zenodo.18256864
  10. Wang, M.; Luo, J.; Lin, K.; Chen, Y.; Huang, X.; Liu, J.; Wang, A.; Xiao, D. Colony-YOLO: A Lightweight Micro-Colony Detection Network Based on Improved YOLOv8n. Microorganisms 2025, 13, 1617. https://doi.org/10.3390/microorganisms13071617
  11. Silva, M., Martinho, D., Marreiros, G. (2026). Deep Learning-Based Microbial Colony Detection on Agar Plates. In: Valente de Oliveira, J., Leite, J., Rodrigues, J., Dias, J., Cardoso, P. (eds) Progress in Artificial Intelligence. EPIA 2025. Lecture Notes in Computer Science(), vol 16121. Springer, Cham. https://doi.org/10.1007/978-3-032-05176-9_4
  12. Sarmis A, Ustebay S, Mutlu MA, Canbaz FA, Kaya GK. Deep Learning-Based Rapid Identification of Escherichia coli and Klebsiella pneumoniae from Chromogenic Agar Urine Cultures Using YOLOv12. Risk Manag Healthc Policy. 2026;19:561761 https://doi.org/10.2147/RMHP.S561761

This paper presents a two-stage deep learning pipeline for automated classification of urinary tract infection (UTI) pathogens from agar plate images. Stage 1 employs YOLO11m for colony detection on full annotated agar plate images from three public datasets. Stage 2 employs EfficientNetV2-M with a custom classifier head (1280→512→5) identifying five clinically significant UTI pathogens: Escherichia coli, Klebsiella pneumoniae, Proteus mirabilis, Pseudomonas aeruginosa, and Staphylococcus aureus.

Keywords : UTI Pathogen Classification; YOLO11; EfficientNetV2-M; Agar Plate Analysis; Bacterial Colony Detection; CLAHE.

Paper Submission Last Date
31 - July - 2026

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