A methodology for texture feature-based quality assessment in nucleus segmentation of histopathology image

Abstract

Context: Image segmentation pipelines often are sensitive to algorithm input parameters. Algorithm parameters optimized for a set of images do not necessarily produce good-quality-segmentation results for other images. Even within an image, some regions may not be well segmented due to a number of factors, including multiple pieces of tissue with distinct characteristics, differences in staining of the tissue, normal versus tumor regions, and tumor heterogeneity. Evaluation of quality of segmentation results is an important step in image analysis. It is very labor intensive to do quality assessment manually with large image datasets because a whole-slide tissue image may have hundreds of thousands of nuclei. Semi-automatic mechanisms are needed to assist researchers and application developers to detect image regions with bad segmentations efficiently. Aims: Our goal is to develop and evaluate a machine-learning-based semi-automated workflow to assess quality of nucleus segmentation results in a large set of whole-slide tissue images. Methods: We propose a quality control methodology, in which machine-learning algorithms are trained with image intensity and texture features to produce a classification model. This model is applied to image patches in a whole-slide tissue image to predict the quality of nucleus segmentation in each patch. The training step of our methodology involves the selection and labeling of regions by a pathologist in a set of images to create the training dataset. The image regions are partitioned into patches. A set of intensity and texture features is computed for each patch. A classifier is trained with the features and the labels assigned by the pathologist. At the end of this process, a classification model is generated. The classification step applies the classification model to unlabeled test images. Each test image is partitioned into patches. The classification model is applied to each patch to predict the patch's label. Results: The proposed methodology has been evaluated by assessing the segmentation quality of a segmentation method applied to images from two cancer types in The Cancer Genome Atlas; WHO Grade II lower grade glioma (LGG) and lung adenocarcinoma (LUAD). The results show that our method performs well in predicting patches with good-quality segmentations and achieves F1 scores 84.7% for LGG and 75.43% for LUAD. Conclusions: As image scanning technologies advance, large volumes of whole-slide tissue images will be available for research and clinical use. Efficient approaches for the assessment of quality and robustness of output from computerized image analysis workflows will become increasingly critical to extracting useful quantitative information from tissue images. Our work demonstrates the feasibility of machine-learning-based semi-automated techniques to assist researchers and algorithm developers in this process.

Keywords

• Classification
• nuclei segmentation quality assessment
• texture feature