Pixel-to-Pixel Learning With Weak Supervision for Single-Stage Nucleus Recognition in Ki67 Images

Abstract

OBJECTIVE: Nucleus recognition is a critical yet challenging step in histopathology image analysis, for example, in Ki67 immunohistochemistry stained images. Although many automated methods have been proposed, most use a multi-stage processing pipeline to categorize nuclei, leading to cumbersome, low-throughput, and error-prone assessments. To address this issue, we propose a novel deep fully convolutional network for single- stage nucleus recognition. METHODS: Instead of conducting direct pixel- wise classification, we formulate nucleus identification as a deep structured regression model. For each input image, it produces multiple proximity maps, each of which corresponds to one nucleus category and exhibits strong responses in central regions of the nuclei. In addition, by taking into consideration the nucleus distribution in histopathology images, we further introduce an auxiliary task, region of interest (ROI) extraction, to assist and boost the nucleus quantification with weak ROI annotation. The proposed network can be learned in an end-to-end, pixel- to-pixel manner for simultaneous nucleus detection and classification. RESULTS: We have evaluated this network on a pancreatic neuroendocrine tumor Ki67 image dataset, and the experiments demonstrate that our method outperforms recent state-of-the-art approaches. CONCLUSION: We present a new, pixel-to-pixel deep neural network with two sibling branches for effective nucleus recognition and observe that learning with another relevant task, ROI extraction, can further boost individual nucleus localization and classification. SIGNIFICANCE: Our method provides a clean, single-stage nucleus recognition pipeline for histopathology image analysis, especially a new perspective for Ki67 image quantification, which would potentially benefit individual object quantification in whole-slide images.