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Deep learning accurately stains digital biopsy slides

#artificialintelligence

Tissue biopsy slides stained using hematoxylin and eosin (H&E) dyes are a cornerstone of histopathology, especially for pathologists needing to diagnose and determine the stage of cancers. A research team led by MIT scientists at the Media Lab, in collaboration with clinicians at Stanford University School of Medicine and Harvard Medical School, now shows that digital scans of these biopsy slides can be stained computationally, using deep learning algorithms trained on data from physically dyed slides. Pathologists who examined the computationally stained H&E slide images in a blind study could not tell them apart from traditionally stained slides while using them to accurately identify and grade prostate cancers. What's more, the slides could also be computationally "de-stained" in a way that resets them to an original state for use in future studies, the researchers conclude in their May 20 study published in JAMA Network. This process of computational digital staining and de-staining preserves small amounts of tissue biopsied from cancer patients and allows researchers and clinicians to analyze slides for multiple kinds of diagnostic and prognostic tests, without needing to extract additional tissue sections.


Strategies for Training Stain Invariant CNNs

arXiv.org Machine Learning

An important part of Digital Pathology is the analysis of multiple digitised whole slide images from differently stained tissue sections. It is common practice to mount consecutive sections containing corresponding microscopic structures on glass slides, and to stain them differently to highlight specific tissue components. These multiple staining modalities result in very different images but include a significant amount of consistent image information. Deep learning approaches have recently been proposed to analyse these images in order to automatically identify objects of interest for pathologists. These supervised approaches require a vast amount of annotations, which are difficult and expensive to acquire---a problem that is multiplied with multiple stainings. This article presents several training strategies that make progress towards stain invariant networks. By training the network on one commonly used staining modality and applying it to images that include corresponding but differently stained tissue structures, the presented unsupervised strategies demonstrate significant improvements over standard training strategies.


Her2 Challenge Contest: A Detailed Assessment of Automated Her2 Scoring Algorithms in Whole Slide Images of Breast Cancer Tissues

arXiv.org Artificial Intelligence

Evaluating expression of the Human epidermal growth factor receptor 2 (Her2) by visual examination of immunohistochemistry (IHC) on invasive breast cancer (BCa) is a key part of the diagnostic assessment of BCa due to its recognised importance as a predictive and prognostic marker in clinical practice. However, visual scoring of Her2 is subjective and consequently prone to inter-observer variability. Given the prognostic and therapeutic implications of Her2 scoring, a more objective method is required. In this paper, we report on a recent automated Her2 scoring contest, held in conjunction with the annual PathSoc meeting held in Nottingham in June 2016, aimed at systematically comparing and advancing the state-of-the-art Artificial Intelligence (AI) based automated methods for Her2 scoring. The contest dataset comprised of digitised whole slide images (WSI) of sections from 86 cases of invasive breast carcinoma stained with both Haematoxylin & Eosin (H&E) and IHC for Her2. The contesting algorithms automatically predicted scores of the IHC slides for an unseen subset of the dataset and the predicted scores were compared with the 'ground truth' (a consensus score from at least two experts). We also report on a simple Man vs Machine contest for the scoring of Her2 and show that the automated methods could beat the pathology experts on this contest dataset. This paper presents a benchmark for comparing the performance of automated algorithms for scoring of Her2. It also demonstrates the enormous potential of automated algorithms in assisting the pathologist with objective IHC scoring.


Unsupervised Color Decomposition Of Histologically Stained Tissue Samples

Neural Information Processing Systems

Accurate spectral decomposition is essential for the analysis and diagnosis of histologically stained tissue sections. In this paper we present the first automated system for performing this decomposition. Wecompare the performance of our system with ground truth data and report favorable results.


CeliacNet: Celiac Disease Severity Diagnosis on Duodenal Histopathological Images Using Deep Residual Networks

arXiv.org Machine Learning

Celiac Disease (CD) is a chronic autoimmune disease that affects the small intestine in genetically predisposed children and adults. Gluten exposure triggers an inflammatory cascade which leads to compromised intestinal barrier function. If this enteropathy is unrecognized, this can lead to anemia, decreased bone density, and, in longstanding cases, intestinal cancer. The prevalence of the disorder is 1% in the United States. An intestinal (duodenal) biopsy is considered the "gold standard" for diagnosis. The mild CD might go unnoticed due to non-specific clinical symptoms or mild histologic features. In our current work, we trained a model based on deep residual networks to diagnose CD severity using a histological scoring system called the modified Marsh score. The proposed model was evaluated using an independent set of 120 whole slide images from 15 CD patients and achieved an AUC greater than 0.96 in all classes. These results demonstrate the diagnostic power of the proposed model for CD severity classification using histological images.