Deep Learning-Assisted Quality Control of Histology Teaching Slides: Detection and Localization of Tissue Fold Artifacts in H&E-Stained Images

Abstract

Background/Objectives: Tissue fold artifacts observed in hematoxylin-eosin (H&E)- stained preparations used in histology education can complicate the assessment of normal tissue architecture and affect students' accurate interpretation of microscopic structures. This study aimed to automatically detect and localize tissue fold artifacts in histology teaching preparations using deep learning methods. Methods: A total of 2127 hematoxylin and eosin (H&E)-stained histological images of brain, kidney, liver, small intestine, and testis tissues obtained at 10 & times; magnification were used in the study. The dataset consisted of 899 clean/artifact-free images and 1228 images containing tissue fold artifacts. Seven deep learning architectures, including convolutional neural networks (CNN)-based models and a vision transformer-based model, were evaluated for image-level classification: ResNet18, ResNet50, DenseNet121, EfficientNet-B0, EfficientNet-B3, ConvNeXt-Tiny, and Swin-Tiny. Classification performance was evaluated using an organ-based testing approach, a slide-level train-test split in which images from the same histological slide group were retained within a single subset, a general image-level 80/20 train-test split, and five-fold cross-validation. A DeepLabV3-ResNet50-based segmentation model was trained using QuPath-prepared masks to determine fold regions at the pixel level. Grad-CAM was used for qualitative visualization and quantitative comparison with manually annotated fold regions. Results: All classification models showed excellent performance overall. The Swin-Tiny model was the most accurate in terms of general image-level classification, scoring 99.06% for accuracy, 99.19% for F1-score, and 99.98% for AUC. In slide-level classification, EfficientNet-B3 showed the best performance in terms of accuracy (99.54%) and AUC (99.99%). No pairwise statistical difference was found among the models using Holm adjustment. In the five-fold cross-validation setting, ResNet50 achieved the best performance with the accuracy of 98.73 +/- 0.54%. In the detailed small-intestine error analysis, classification accuracy was 67.67%, with high sensitivity (98.59%) but low specificity (24.34%), mainly because of false-positive predictions. In the segmentation evaluation, the final DeepLabV3-ResNet50 model trained with combined BCE + Dice loss resulted in Dice of 0.7630 +/- 0.2425 and IoU of 0.6661 +/- 0.2577 on the independent test set. False positive segmentations were rare in 899 artifact-free images (only 0.33% of images had a tissue fold region of at least 1%). The quantitative Grad-CAM analysis showed poor spatial agreement with the manually annotated tissue fold masks (Dice = 0.2423; IoU = 0.1441). In the independent MPP10 dataset, ResNet50 achieved 89.63% accuracy and 88.49% F1-score. Conclusions: The suggested method was able to detect tissue fold artifacts as well as localize them in the teaching images of histology. The strong performance recorded at the slide level validates the internal findings, but the limited performance in the case of small intestine images and on the external dataset reveals that tissue structure remains a crucial factor.