Automated Histology Analysis: Opportunities for Signal Processing

<p>Histology is the microscopic inspection of plant or animal tissue. It is a critical component in diagnostic medicine and a tool for studying the pathogenesis and biology of processes such as cancer and embryogenesis. Tissue processing for histology has become increasingly automated, drastically increasing the speed at which histology labs can produce tissue slides for viewing. Another trend is the digitization of these slides, allowing them to be viewed on a computer rather than through a microscope. Despite these changes, much of the routine analysis of tissue sections remains a painstaking, manual task that can only be completed by highly trained pathologists at a high cost per hour. There is, therefore, a niche for image analysis methods that can automate some aspects of this analysis. These methods could also automate tasks that are prohibitively time-consuming for humans, e.g., discovering new disease markers from hundreds of whole-slide images (WSIs) or precisely quantifying tissues within a tumor.</p

Classification with reject option using contextual information

<p>We propose a new algorithm for classification that merges classification with reject option with classification using contextual information. A reject option is desired in many image-classification applications requiring a robust classifier and when the need for high classification accuracy surpasses the need to classify the entire image. Moreover, our algorithm improves the classifier performance by including local and nonlocal contextual information, at the expense of rejecting a fraction of the samples. As a probabilistic model, we adopt a multinomial logistic regression. We use a discriminative random model for the description of the problem; we introduce reject option into the classification problem through association potential, and contextual information through interaction potential. We validate the method on the images of H&E-stained teratoma tissues and show the increase in the classifier performance when rejecting part of the assigned class labels.</p

Algorithm and benchmark dataset for stain separation in histology images

<p>In this work, we present a new algorithm and benchmark dataset for stain separation in histology images. Histology is a critical and ubiquitous task in medical practice and research, serving as a gold standard of diagnosis for many diseases. Automating routine histology analysis tasks could reduce health care costs and improve diagnostic accuracy. One challenge in automation is that histology slides vary in their stain intensity and color; we therefore seek a digital method to normalize the appearance of histology images. As histology slides often have multiple stains on them that must be normalized independently, stain separation must occur before normalization. We propose a new digital stain separation method for the universally-used hematoxylin and eosin stain; this method improves on the state-of-the-art by adjusting the contrast of its eosin-only estimate and including a notion of stain interaction. To validate this method, we have collected a new benchmark dataset via chemical destaining containing ground truth images for stain separation, which we release publicly. Our experiments show that our method achieves more accurate stain separation than two comparison methods and that this improvement in separation accuracy leads to improved normalization.</p

A domain-knowledge-inspired mathematical framework for the description and classification of H&E stained histopathology images.

We present the current state of our work on a mathematical framework for identification and delineation of histopathology images-local histograms and occlusion models. Local histograms are histograms computed over defined spatial neighborhoods whose purpose is to characterize an image locally. This unit of description is augmented by our occlusion models that describe a methodology for image formation. In the context of this image formation model, the power of local histograms with respect to appropriate families of images will be shown through various proved statements about expected performance. We conclude by presenting a preliminary study to demonstrate the power of the framework in the context of histopathology image classification tasks that, while differing greatly in application, both originate from what is considered an appropriate class of images for this framework.</p

A vocabulary for the identification and delineation of teratoma tissue components in hematoxylin and eosin-stained samples.

<p>We propose a methodology for the design of features mimicking the visual cues used by pathologists when identifying tissues in hematoxylin and eosin (H&E)-stained samples.</p> <p>BACKGROUND: H&E staining is the gold standard in clinical histology; it is cheap and universally used, producing a vast number of histopathological samples. While pathologists accurately and consistently identify tissues and their pathologies, it is a time-consuming and expensive task, establishing the need for automated algorithms for improved throughput and robustness.</p> <p>METHODS: We use an iterative feedback process to design a histopathology vocabulary (HV), a concise set of features that mimic the visual cues used by pathologists, e.g. "cytoplasm color" or "nucleus density". These features are based in histology and understood by both pathologists and engineers. We compare our HV to several generic texture-feature sets in a pixel-level classification algorithm.</p> <p>RESULTS: Results on delineating and identifying tissues in teratoma tumor samples validate our expert knowledge-based approach.</p> <p>CONCLUSIONS: The HV can be an effective tool for identifying and delineating teratoma components from images of H&E-stained tissue samples.</p

Automatic identification and delineation of germ layer components in H&E stained images of teratomas derived from human and nonhuman primate embryonic stem cells

We present a methodology for the automatic identification and delineation of germ-layer components in H&E stained images of teratomas derived from human and nonhuman primate embryonic stem cells. A knowledge and understanding of the biology of these cells may lead to advances in tissue regeneration and repair, the treatment of genetic and developmental syndromes, and drug testing and discovery. As a teratoma is a chaotic organization of tissues derived from the three primary embryonic germ layers, H&E teratoma images often present multiple tissues, each of having complex and unpredictable positions, shapes, and appearance with respect to each individual tissue as well as with respect to other tissues. While visual identification of these tissues is time-consuming, it is surprisingly accurate, indicating that there exist enough visual cues to accomplish the task. We propose automatic identification and delineation of these tissues by mimicking these visual cues. We use pixel-based classification, resulting in an encouraging range of classification accuracies from 74.9% to 93.2% for 2- to 5-tissue classification experiments at different scales.</p