An investigation into augmentation and preprocessing for optimising X-ray classification in limited datasets: a case study on necrotising enterocolitis

• Published in: International journal for computer assisted radiology and surgery 2024, Vol.19 (6), p.1223-1231
• Main Authors: Nowak, Franciszek, Yung, Ka-Wai, Sivaraj, Jayaram, De Coppi, Paolo, Stoyanov, Danail, Loukogeorgakis, Stavros, Mazomenos, Evangelos B.
• Format: Article
• Language: English
• Subjects: Accuracy; Classification; Color; Computer Imaging; Computer Science; Data augmentation; Datasets; Diagnosis; Diagnosis, Computer-Assisted - methods; Enterocolitis, Necrotizing - classification; Enterocolitis, Necrotizing - diagnosis; Enterocolitis, Necrotizing - diagnostic imaging; Female; Health Informatics; Humans; Imaging; Infant, Newborn; Infant, Premature; Investigations; Machine learning; Medical imaging; Medicine; Medicine & Public Health; Occlusion; Original; Original Article; Pattern Recognition and Graphics; Performance enhancement; Pipelines; Preprocessing; Radiographic Image Interpretation, Computer-Assisted - methods; Radiography, Abdominal - methods; Radiology; Robustness (mathematics); Surgery; Vision; X-rays
• ISSN: 1861-6429; 1861-6410; 1861-6429
• DOI: 10.1007/s11548-024-03107-0

Purpose Obtaining large volumes of medical images, required for deep learning development, can be challenging in rare pathologies. Image augmentation and preprocessing offer viable solutions. This work explores the case of necrotising enterocolitis (NEC), a rare but life-threatening condition affecting premature neonates, with challenging radiological diagnosis. We investigate data augmentation and preprocessing techniques and propose two optimised pipelines for developing reliable computer-aided diagnosis models on a limited NEC dataset. Methods We present a NEC dataset of 1090 Abdominal X-rays (AXRs) from 364 patients and investigate the effect of geometric augmentations, colour scheme augmentations and their combination for NEC classification based on the ResNet-50 backbone. We introduce two pipelines based on colour contrast and edge enhancement, to increase the visibility of subtle, difficult-to-identify, critical NEC findings on AXRs and achieve robust accuracy in a challenging three-class NEC classification task. Results Our results show that geometric augmentations improve performance, with Translation achieving +6.2%, while Flipping and Occlusion decrease performance. Colour augmentations, like Equalisation, yield modest improvements. The proposed Pr-1 and Pr-2 pipelines enhance model accuracy by +2.4% and +1.7%, respectively. Combining Pr-1/Pr-2 with geometric augmentation, we achieve a maximum performance increase of 7.1%, achieving robust NEC classification. Conclusion Based on an extensive validation of preprocessing and augmentation techniques, our work showcases the previously unreported potential of image preprocessing in AXR classification tasks with limited datasets. Our findings can be extended to other medical tasks for designing reliable classifier models with limited X-ray datasets. Ultimately, we also provide a benchmark for automated NEC detection and classification from AXRs.