Dataset Information

Nuclear Segmentation in Histopathological Images Using Two-Stage Stacked U-Nets With Attention Mechanism.

ABSTRACT: Nuclei segmentation is a fundamental but challenging task in histopathological image analysis. One of the main problems is the existence of overlapping regions which increases the difficulty of independent nuclei separation. In this study, to solve the segmentation of nuclei and overlapping regions, we introduce a nuclei segmentation method based on two-stage learning framework consisting of two connected Stacked U-Nets (SUNets). The proposed SUNets consists of four parallel backbone nets, which are merged by the attention generation model. In the first stage, a Stacked U-Net is utilized to predict pixel-wise segmentation of nuclei. The output binary map together with RGB values of the original images are concatenated as the input of the second stage of SUNets. Due to the sizable imbalance of overlapping and background regions, the first network is trained with cross-entropy loss, while the second network is trained with focal loss. We applied the method on two publicly available datasets and achieved state-of-the-art performance for nuclei segmentation-mean Aggregated Jaccard Index (AJI) results were 0.5965 and 0.6210, and F1 scores were 0.8247 and 0.8060, respectively; our method also segmented the overlapping regions between nuclei, with average AJI = 0.3254. The proposed two-stage learning framework outperforms many current segmentation methods, and the consistent good segmentation performance on images from different organs indicates the generalized adaptability of our approach.

SUBMITTER: Kong Y

PROVIDER: S-EPMC7649338 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Nuclear Segmentation in Histopathological Images Using Two-Stage Stacked U-Nets With Attention Mechanism.

Kong Yan Y Genchev Georgi Z GZ Wang Xiaolei X Zhao Hongyu H Lu Hui H

Frontiers in bioengineering and biotechnology 20201026

Nuclei segmentation is a fundamental but challenging task in histopathological image analysis. One of the main problems is the existence of overlapping regions which increases the difficulty of independent nuclei separation. In this study, to solve the segmentation of nuclei and overlapping regions, we introduce a nuclei segmentation method based on two-stage learning framework consisting of two connected Stacked U-Nets (SUNets). The proposed SUNets consists of four parallel backbone nets, which ...[more]

PMID: 33195135

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Project description:Algorithmic segmentation of histologically relevant regions of tissues in digitized histopathological images is a critical step towards computer-assisted diagnosis and analysis. For example, automatic identification of epithelial and stromal tissues in images is important for spatial localisation and guidance in the analysis and characterisation of tumour micro-environment. Current segmentation approaches are based on supervised methods, which require extensive training data from high quality, manually annotated images. This is often difficult and costly to obtain. This paper presents an alternative data-independent framework based on unsupervised segmentation of oropharyngeal cancer tissue micro-arrays (TMAs). An automated segmentation algorithm based on mathematical morphology is first applied to light microscopy images stained with haematoxylin and eosin. This partitions the image into multiple binary 'virtual-cells', each enclosing a potential 'nucleus' (dark basins in the haematoxylin absorbance image). Colour and morphology measurements obtained from these virtual-cells as well as their enclosed nuclei are input into an advanced unsupervised learning model for the identification of epithelium and stromal tissues. Here we exploit two Consensus Clustering (CC) algorithms for the unsupervised recognition of tissue compartments, that consider the consensual opinion of a group of individual clustering algorithms. Unlike most unsupervised segmentation analyses, which depend on a single clustering method, the CC learning models allow for more robust and stable detection of tissue regions. The proposed framework performance has been evaluated on fifty-five hand-annotated tissue images of oropharyngeal tissues. Qualitative and quantitative results of the proposed segmentation algorithm compare favourably with eight popular tissue segmentation strategies. Furthermore, the unsupervised results obtained here outperform those obtained with individual clustering algorithms.

Project description:ObjectivesAnterior mediastinal disease is a common disease in the chest. Computed tomography (CT), as an important imaging technology, is widely used in the diagnosis of mediastinal diseases. Doctors find it difficult to distinguish lesions in CT images because of image artifact, intensity inhomogeneity, and their similarity with other tissues. Direct segmentation of lesions can provide doctors a method to better subtract the features of the lesions, thereby improving the accuracy of diagnosis.MethodAs the trend of image processing technology, deep learning is more accurate in image segmentation than traditional methods. We employ a two-stage 3D ResUNet network combined with lung segmentation to segment CT images. Given that the mediastinum is between the two lungs, the original image is clipped through the lung mask to remove some noises that may affect the segmentation of the lesion. To capture the feature of the lesions, we design a two-stage network structure. In the first stage, the features of the lesion are learned from the low-resolution downsampled image, and the segmentation results under a rough scale are obtained. The results are concatenated with the original image and encoded into the second stage to capture more accurate segmentation information from the image. In addition, attention gates are introduced in the upsampling of the network, and these gates can focus on the lesion and play a role in filtering the features. The proposed method has achieved good results in the segmentation of the anterior mediastinal.ResultsThe proposed method was verified on 230 patients, and the anterior mediastinal lesions were well segmented. The average Dice coefficient reached 87.73%. Compared with the model without lung segmentation, the model with lung segmentation greatly improved the accuracy of lesion segmentation by approximately 9%. The addition of attention gates slightly improved the segmentation accuracy.ConclusionThe proposed automatic segmentation method has achieved good results in clinical data. In clinical application, automatic segmentation of lesions can assist doctors in the diagnosis of diseases and may facilitate the automated diagnosis of illnesses in the future.

Dataset Information

Nuclear Segmentation in Histopathological Images Using Two-Stage Stacked U-Nets With Attention Mechanism.

Publications

Nuclear Segmentation in Histopathological Images Using Two-Stage Stacked U-Nets With Attention Mechanism.

Similar Datasets

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