Lena Kajland Wilén

Nikolay Burlutskiy, Nicolas Pinchaud, Feng Gu et al.

Gleason grading specified in ISUP 2014 is the clinical standard in staging prostate cancer and the most important part of the treatment decision. However, the grading is subjective and suffers from high intra and inter-user variability. To improve the consistency and objectivity in the grading, we introduced glandular tissue WithOut Basal cells (WOB) as the ground truth. The presence of basal cells is the most accepted biomarker for benign glandular tissue and the absence of basal cells is a strong indicator of acinar prostatic adenocarcinoma, the most common form of prostate cancer. Glandular tissue can objectively be assessed as WOB or not WOB by using specific immunostaining for glandular tissue (Cytokeratin 8/18) and for basal cells (Cytokeratin 5/6 + p63). Even more, WOB allowed us to develop a semi-automated data generation pipeline to speed up the tremendously time consuming and expensive process of annotating whole slide images by pathologists. We generated 295 prostatectomy images exhaustively annotated with WOB. Then we used our Deep Learning Framework, which achieved the $2^{nd}$ best reported score in Camelyon17 Challenge, to train networks for segmenting WOB in needle biopsies. Evaluation of the model on 63 needle biopsies showed promising results which were improved further by finetuning the model on 118 biopsies annotated with WOB, achieving F1-score of 0.80 and Precision-Recall AUC of 0.89 at the pixel-level. Then we compared the performance of the model against 17 biopsies annotated independently by 3 pathologists using only H\&E staining. The comparison demonstrated that the model performed on a par with the pathologists. Finally, the model detected and accurately outlined existing WOB areas in two biopsies incorrectly annotated as totally WOB-free biopsies by three pathologists and in one biopsy by two pathologists.

Nikolay Burlutskiy, Feng Gu, Lena Kajland Wilen et al.

We developed a deep learning framework that helps to automatically identify and segment lung cancer areas in patients' tissue specimens. The study was based on a cohort of lung cancer patients operated at the Uppsala University Hospital. The tissues were reviewed by lung pathologists and then the cores were compiled to tissue micro-arrays (TMAs). For experiments, hematoxylin-eosin stained slides from 712 patients were scanned and then manually annotated. Then these scans and annotations were used to train segmentation models of the developed framework. The performance of the developed deep learning framework was evaluated on fully annotated TMA cores from 178 patients reaching pixel-wise precision of 0.80 and recall of 0.86. Finally, publicly available Stanford TMA cores were used to demonstrate high performance of the framework qualitatively.

Feng Gu, Nikolay Burlutskiy, Mats Andersson et al.

Digital pathology provides an excellent opportunity for applying fully convolutional networks (FCNs) to tasks, such as semantic segmentation of whole slide images (WSIs). However, standard FCNs face challenges with respect to multi-resolution, inherited from the pyramid arrangement of WSIs. As a result, networks specifically designed to learn and aggregate information at different levels are desired. In this paper, we propose two novel multi-resolution networks based on the popular `U-Net' architecture, which are evaluated on a benchmark dataset for binary semantic segmentation in WSIs. The proposed methods outperform the U-Net, demonstrating superior learning and generalization capabilities.