High-throughput phenotyping of nematode cysts

There are a huge number of features which are said to improve Convolutional Neural Network (CNN) accuracy. Practical testing of combinations of such features on large datasets, and theoretical justification of the result, is required. Some features operate on certain models exclusively and for certain problems exclusively, or only for small-scale datasets; while some features, such as batch-normalization and residual-connections, are applicable to the majority of models, tasks, and datasets. We assume that such universal features include Weighted-Residual-Connections (WRC), Cross-Stage-Partial-connections (CSP), Cross mini-Batch Normalization (CmBN), Self-adversarial-training (SAT) and Mish-activation. We use new features: WRC, CSP, CmBN, SAT, Mish activation, Mosaic data augmentation, CmBN, DropBlock regularization, and CIoU loss, and combine some of them to achieve state-of-the-art results: 43.5% AP (65.7% AP50) for the MS COCO dataset at a realtime speed of ~65 FPS on Tesla V100. Source code is at https://github.com/AlexeyAB/darknet

Nuclear segmentation in digital microscopic tissue images can enable extraction of high-quality features for nuclear morphometrics and other analysis in computational pathology. Conventional image processing techniques, such as Otsu thresholding and watershed segmentation, do not work effectively on challenging cases, such as chromatin-sparse and crowded nuclei. In contrast, machine learning-based segmentation can generalize across various nuclear appearances. However, training machine learning algorithms requires data sets of images, in which a vast number of nuclei have been annotated. Publicly accessible and annotated data sets, along with widely agreed upon metrics to compare techniques, have catalyzed tremendous innovation and progress on other image classification problems, particularly in object recognition. Inspired by their success, we introduce a large publicly accessible data set of hematoxylin and eosin (H&E)-stained tissue images with more than 21000 painstakingly annotated nuclear boundaries, whose quality was validated by a medical doctor. Because our data set is taken from multiple hospitals and includes a diversity of nuclear appearances from several patients, disease states, and organs, techniques trained on it are likely to generalize well and work right out-of-the-box on other H&E-stained images. We also propose a new metric to evaluate nuclear segmentation results that penalizes object- and pixel-level errors in a unified manner, unlike previous metrics that penalize only one type of error. We also propose a segmentation technique based on deep learning that lays a special emphasis on identifying the nuclear boundaries, including those between the touching or overlapping nuclei, and works well on a diverse set of test images.