Antibody Supervised Training of a Deep Learning Based Algorithm for Leukocyte Segmentation in Papillary Thyroid Carcinoma

• Published in: IEEE journal of biomedical and health informatics Vol. 25; no. 2; pp. 422 - 428
• Main Authors: Stenman, Sebastian, Bychkov, Dmitrii, Kucukel, Hakan, Linder, Nina, Haglund, Caj, Arola, Johanna, Lundin, Johan
• Format: Journal Article
• Language: English
• Published: United States IEEE 01-02-2021; The Institute of Electrical and Electronics Engineers, Inc. (IEEE)
• Subjects: Algorithms; Annotations; Antibodies; antibody-supervised learning; Antigens; artificial neural network; Artificial neural networks; Cancer; CD45 antigen; Deep learning; Digital pathology; Ground truth; Image segmentation; Immune system; Leukocytes; Masks; Medicin och hälsovetenskap; Neural networks; Papillary thyroid carcinoma; Prediction algorithms; Protocols; Thyroid; Thyroid cancer; Tiles; Tissues; Training; tumor-infiltrating lymphocytes
• ISSN: 2168-2194; 2168-2208; 2168-2208
• DOI: 10.1109/JBHI.2020.2994970

The quantity of leukocytes in papillary thyroid carcinoma (PTC) potentially have prognostic and treatment predictive value. Here, we propose a novel method for training a convolutional neural network (CNN) algorithm for segmenting leukocytes in PTCs. Tissue samples from two retrospective PTC cohort were obtained and representative tissue slides from twelve patients were stained with hematoxylin and eosin (HE) and digitized. Then, the HE slides were destained and restained immunohistochemically (IHC) with antibodies to the pan-leukocyte anti CD45 antigen and scanned again. The two stain-pairs of all representative tissue slides were registered, and image tiles of regions of interests were exported. The image tiles were processed and the 3,3′-diaminobenzidine (DAB) stained areas representing anti CD45 expression were turned into binary masks. These binary masks were applied as annotations on the HE image tiles and used in the training of a CNN algorithm. Ten whole slide images (WSIs) were used for training using a five-fold cross-validation and the remaining two slides were used as an independent test set for the trained model. For visual evaluation, the algorithm was run on all twelve WSIs, and in total 238,144 tiles sized 500 × 500 pixels were analyzed. The trained CNN algorithm had an intersection over union of 0.82 for detection of leukocytes in the HE image tiles when comparing the prediction masks to the ground truth anti CD45 mask. We conclude that this method for generating antibody supervised annotations using the destain-restain IHC guided annotations resulted in high accuracy segmentations of leukocytes in HE tissue images.