Bacterial image analysis using multi-task deep learning approaches for clinical microscopy

Abstract

Background Bacterial image analysis plays a vital role in various fields, providing valuable information and insights for studying bacterial structural biology, diagnosing and treating infectious diseases caused by pathogenic bacteria, discovering and developing drugs that can combat bacterial infections, etc. As a result, it has prompted efforts to automate bacterial image analysis tasks. By automating analysis tasks and leveraging more advanced computational techniques, such as deep learning (DL) algorithms, bacterial image analysis can contribute to rapid, more accurate, efficient, reliable, and standardised analysis, leading to enhanced understanding, diagnosis, and control of bacterial-related phenomena. Methods Three object detection networks of DL algorithms, namely SSD-MobileNetV2, EfficientDet, and YOLOv4, were developed to automatically detect Escherichia coli (E. coli) bacteria from microscopic images. The multi-task DL framework is developed to classify the bacteria according to their respective growth stages, which include rod-shaped cells, dividing cells, and microcolonies. Data preprocessing steps were carried out before training the object detection models, including image augmentation, image annotation, and data splitting. The performance of the DL techniques is evaluated using the quantitative assessment method based on mean average precision (mAP), precision, recall, and F1-score. The performance metrics of the models were compared and analysed. The best DL model was then selected to perform multi-task object detections in identifying rod-shaped cells, dividing cells, and microcolonies. Results The output of the test images generated from the three proposed DL models displayed high detection accuracy, with YOLOv4 achieving the highest confidence score range of detection and being able to create different coloured bounding boxes for different growth stages of E. coli bacteria. In terms of statistical analysis, among the three proposed models, YOLOv4 demonstrates superior performance, achieving the highest mAP of 98% with the highest precision, recall, and F1-score of 86%, 97%, and 91%, respectively. Conclusions This study has demonstrated the effectiveness, potential, and applicability of DL approaches in multi-task bacterial image analysis, focusing on automating the detection and classification of bacteria from microscopic images. The proposed models can output images with bounding boxes surrounding each detected E. coli bacteria, labelled with their growth stage and confidence level of detection. All proposed object detection models have achieved promising results, with YOLOv4 outperforming the other models.