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FFPE plus plus : Improving the quality of formalin-fixed paraffin-embedded tissue imaging via contrastive unpaired image-to-image translation

2024    Kassab, Mohamad; Jehanzaib, Muhammad; Basak, Kayhan; Demir, Derya; Keles, G. Evren; Turan, Mehmet

Formalin-fixation and paraffin-embedding (FFPE) is a technique for preparing and preserving tissue specimens that has been utilized in histopathology since the late 19th century. This process is further complicated by FFPE preparation steps such as fixation, processing, embedding, microtomy, staining, and coverslipping, which often results in artifacts due to the complex histological and cytological characteristics of a tissue specimen. The term "artifacts"includes, but is not limited to, staining inconsistencies, tissue folds, chattering, pen marks, blurring, air bubbles, and contamination. The presence of artifacts may interfere with pathological diagnosis in disease detection, subtyping, grading, and choice of therapy. In this study, we propose FFPE++, an unpaired image to-image translation method based on contrastive learning with a mixed channel-spatial attention module and self-regularization loss that drastically corrects the aforementioned artifacts in FFPE tissue sections. Turing tests were performed by 10 board-certified pathologists with more than 10 years of experience. These tests which were performed for ovarian carcinoma, lung adenocarcinoma, lung squamous cell carcinoma, and papillary thyroid carcinoma, demonstrate the clear superiority of the proposed method in many clinical aspects compared with standard FFPE images. Based on the qualitative experiments and feedback from the Turing tests, we believe that FFPE++ can contribute to substantial diagnostic and prognostic accuracy in clinical pathology in the future and can also improve the performance of AI tools in digital pathology. The code and dataset are publicly available at https://github.com/DeepMIALab/FFPEPlus.