Using an Anomaly Detection Approach for the Segmentation of Colorectal Cancer Tumors in Whole Slide Images

Colorectal cancer (CRC) is the 2nd most commonly diagnosed cancer in the United States. Genetic testing is critical in assisting in the early detection of CRC and selection of individualized treatment plans, which have shown to improve the survival rate of CRC patients. The tissue slides review (TSR), a tumor tissue macro-dissection procedure, is a required pre-analytical step to perform genetic testing. Due to the subjective nature of the process, major discrepancies in CRC diagnostics by pathologists are reported, and metrics for quality are often only qualitative. Progressive context encoder anomaly detection (P-CEAD) is an anomaly detection approach to detect tumor tissue from Whole Slide Images (WSIs), since tumor tissue is by its nature, an anomaly. P-CEAD-based CRC tumor segmentation achieves a 71% ±26% sensitivity, 92% ±7% specificity, and 63% ±23% F1 score. The proposed approach provides an automated CRC tumor segmentation pipeline with a quantitatively reproducible quality compared with the conventional manual tumor segmentation procedure. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This work was funded by the Mayo Clinic Digital Pathology Program, and the University of Minnesota Graduate School Doctoral Dissertation Fellowship for the year of 2022-2023. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The Institutional Review Board of the Mayo Clinic gave approval of this study. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes All data produced in the present study are available upon reasonable request to the authors