Deep learning-based histopathological segmentation for whole slide images of colorectal cancer in a compressed domain

• Published in: Scientific reports Vol. 11; no. 1; p. 22520
• Main Authors: Kim, Hyeongsub, Yoon, Hongjoon, Thakur, Nishant, Hwang, Gyoyeon, Lee, Eun Jung, Kim, Chulhong, Chong, Yosep
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 18.11.2021; Nature Publishing Group; Nature Portfolio
• Subjects: 631/114/1305; 631/114/1564; 639/705/117; Algorithms; Biopsy; Colorectal cancer; Colorectal carcinoma; Colorectal Neoplasms - diagnostic imaging; Computer Graphics; Computers; Deep Learning; Humanities and Social Sciences; Humans; Image processing; Image Processing, Computer-Assisted - methods; Machine Learning; multidisciplinary; Neural networks; Neural Networks, Computer; Pattern recognition; Predictive Value of Tests; Principal Component Analysis; Principal components analysis; Probability; Reproducibility of Results; Science; Science (multidisciplinary); Segmentation; Software; User-Computer Interface; Wavelet Analysis; Wavelet transforms
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-021-01905-z

Automatic pattern recognition using deep learning techniques has become increasingly important. Unfortunately, due to limited system memory, general preprocessing methods for high-resolution images in the spatial domain can lose important data information such as high-frequency information and the region of interest. To overcome these limitations, we propose an image segmentation approach in the compressed domain based on principal component analysis (PCA) and discrete wavelet transform (DWT). After inference for each tile using neural networks, a whole prediction image was reconstructed by wavelet weighted ensemble (WWE) based on inverse discrete wavelet transform (IDWT). The training and validation were performed using 351 colorectal biopsy specimens, which were pathologically confirmed by two pathologists. For 39 test datasets, the average Dice score, the pixel accuracy, and the Jaccard score were 0.804 ± 0.125, 0.957 ± 0.025, and 0.690 ± 0.174, respectively. We can train the networks for the high-resolution image with the large region of interest compared to the result in the low-resolution and the small region of interest in the spatial domain. The average Dice score, pixel accuracy, and Jaccard score are significantly increased by 2.7%, 0.9%, and 2.7%, respectively. We believe that our approach has great potential for accurate diagnosis.