Background Helicobacter pylori, a 2 × 1 μm spiral-shaped bacterium, is the most common risk factor for gastric cancer worldwide. Clinically, patients presenting with symptoms of gastritis, routinely undergo gastric biopsies. The following histo-morphological evaluation dictates therapeutic decisions, where antibiotics are used for H. pylori eradication. There is a strong rational to accelerate the detection process of H. pylori on histological specimens, using novel technologies, such as deep learning. Methods We designed a deep-learning-based decision support algorithm that can be applied on regular whole slide images of gastric biopsies. In detail, we can detect H. pylori both on Giemsa- and regular H&E stained whole slide images. Results With the help of our decision support algorithm, we show an increased sensitivity in a subset of 87 cases that underwent additional PCR- and immunohistochemical testing to define a sensitive ground truth of HP presence. For Giemsa stained sections, the decision support algorithm achieved a sensitivity of 100% compared to 68.4% (microscopic diagnosis), with a tolerable specificity of 66.2% for the decision support algorithm compared to 92.6 (microscopic diagnosis). Conclusion Together, we provide the first evidence of a decision support algorithm proving as a sensitive screening option for H. pylori that can potentially aid pathologists to accurately diagnose H. pylori presence on gastric biopsies.
Histopathological evaluation of tissue samples is a key practice in patient diagnosis and drug development, especially in oncology. Historically, Hematoxylin and Eosin (H&E) has been used by pathologists as a gold standard staining. However, in many cases, various target specific stains, including immunohistochemistry (IHC), are needed in order to highlight specific structures in the tissue. As tissue is scarce and staining procedures are tedious, it would be beneficial to generate images of stained tissue virtually. Virtual staining could also generate in-silico multiplexing of different stains on the same tissue segment. In this paper, we present a sample application that generates FAP-CK virtual IHC images from Ki67-CD8 real IHC images using an unsupervised deep learning approach based on CycleGAN. We also propose a method to deal with tiling artifacts caused by normalization layers and we validate our approach by comparing the results of tissue analysis algorithms for virtual and real images.
Breast cancer is the most common malignancy in women worldwide, and is responsible for more than half a million deaths each year. The appropriate therapy depends on the evaluation of the expression of various biomarkers, such as the human epidermal growth factor receptor 2 (HER2) transmembrane protein, through specialized techniques, such as immunohistochemistry or in situ hybridization. In this work, we present the HER2 on hematoxylin and eosin (HEROHE) challenge, a parallel event of the 16th European Congress on Digital Pathology, which aimed to predict the HER2 status in breast cancer based only on hematoxylin–eosin-stained tissue samples, thus avoiding specialized techniques. The challenge consisted of a large, annotated, whole-slide images dataset (509), specifically collected for the challenge. Models for predicting HER2 status were presented by 21 teams worldwide. The best-performing models are presented by detailing the network architectures and key parameters. Methods are compared and approaches, core methodologies, and software choices contrasted. Different evaluation metrics are discussed, as well as the performance of the presented models for each of these metrics. Potential differences in ranking that would result from different choices of evaluation metrics highlight the need for careful consideration at the time of their selection, as the results show that some metrics may misrepresent the true potential of a model to solve the problem for which it was developed. The HEROHE dataset remains publicly available to promote advances in the field of computational pathology.
A key challenge in cancer immunotherapy biomarker research is quantification of pattern changes in microscopic whole slide images of tumor biopsies. Different cell types tend to migrate into various tissue compartments and form variable distribution patterns. Drug development requires correlative analysis of various biomarkers in and between the tissue compartments. To enable that, tissue slides are manually annotated by expert pathologists. Manual annotation of tissue slides is a labor intensive, tedious and error-prone task. Automation of this annotation process can improve accuracy and consistency while reducing workload and cost in a way that will positively influence drug development efforts. In this paper we present a novel one-shot color deconvolution deep learning method to automatically segment and annotate digitized slide images with multiple stainings into compartments of tumor, healthy tissue, and necrosis. We address the task in the context of drug development where multiple stains, tissue and tumor types exist and look into solutions for generalizations over these image populations.
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