Comprehensive Assessment of CNN Sensitivity in Automated Microorganism Classification: Effects of Compression, Non-Uniform Scaling, and Data Augmentation

Background: The growing demand for automated microorganism classification in the context of Laboratory 4.0 highlights the potential of convolutional neural networks (CNNs) for accurate and efficient image analysis. However, their effectiveness remains limited by the scarcity of large, labeled datasets. This study addresses a key gap in the literature by investigating how commonly used image preprocessing techniques, such as lossy compression, non-uniform scaling (typically applied to fit input images to CNN input layers), and data augmentation, affect the performance of CNNs in automated microorganism classification. Methods: Using two well-established CNN architectures, AlexNet and DenseNet-121, both frequently applied in biomedical image analysis, we conducted a series of computational experiments on a standardized dataset of high-resolution bacterial images. Results: Our results demonstrate under which conditions these preprocessing strategies degrade or improve CNN performance. Using the findings from this research to optimize hyperparameters and train the CNNs, we achieved classification accuracies of 98.61% with AlexNet and 99.82% with DenseNet-121, surpassing the performance reported in current state-of-the-art studies. Conclusions: This study advances laboratory digitalization by reducing data preparation effort, training time, and computational costs, while improving the accuracy of microorganism classification with deep learning. Its contributions also benefit broader biomedical fields such as automated diagnostics, digital pathology, clinical decision support, and point-of-care imaging.