Nuclei Segmentation Approach for Computer Aided Diagnosis

Tumor grading model employing geometric analysis of histopathological images with characteristic nuclei dictionary

Obtaining animal regions and the relative position relationship of animals in the scene is conducive to further studying animal habits, which is of great significance for smart animal farming. However, the complex breeding environment still makes detection difficult. To address the problems of poor target segmentation effects and the weak generalization ability of existing semantic segmentation models in complex scenes, a semantic segmentation model based on an improved DeepLabV3+ network (Imp-DeepLabV3+) was proposed. Firstly, the backbone network of the DeepLabV3+ model was replaced by MobileNetV2 to enhance the feature extraction capability of the model. Then, the layer-by-layer feature fusion method was adopted in the Decoder stage to integrate high-level semantic feature information with low-level high-resolution feature information at multi-scale to achieve more precise up-sampling operation. Finally, the SENet module was further introduced into the network to enhance information interaction after feature fusion and improve the segmentation precision of the model under complex datasets. The experimental results demonstrate that the Imp-DeepLabV3+ model achieved a high pixel accuracy (PA) of 99.4%, a mean pixel accuracy (MPA) of 98.1%, and a mean intersection over union (MIoU) of 96.8%. Compared to the original DeepLabV3+ model, the segmentation performance of the improved model significantly improved. Moreover, the overall segmentation performance of the Imp-DeepLabV3+ model surpassed that of other commonly used semantic segmentation models, such as Fully Convolutional Networks (FCNs), Lite Reduced Atrous Spatial Pyramid Pooling (LR-ASPP), and U-Net. Therefore, this study can be applied to the field of scene segmentation and is conducive to further analyzing individual information and promoting the development of intelligent animal farming.

Artificial Intelligence-Powered Digital Pathology to Improve Diagnosis and Personalized Prognostic Assessment in Patient with Myeloid Neoplasms

Nuclei Segmentation is a very essential and intermediate step for automatic cancer detection from H and E stained histopathology images. In the recent advent, the rise of Convolutional Neural Network (CNN), has enabled researchers to detect nuclei automatically from histopathology images with higher accuracy. However, the performance of automatic nuclei segmentation by CNN is fraught with overfitting, due to very less number of annotated segmented images available. Indeed, we find that the problem of nuclei segmentation is an unsupervised problem, because still now there is no automatic tool available which can make annotated images (nuclei segmented images) accurately, to the best of our knowledge. In this research article, we present a Logarithmic-Base2 of Gaussian (Log-Base2-G) Kernel which has the ability to track only the nuclei portions automatically from Colorectal Cancer H and E stained histopathology images. First, Log-Base2-G Kernel is applied to the input images. Thereafter, we apply an adaptive Canny Edge detector, in order to segment only the nuclei edges from H and E stained histopathology images. Experimental results revealed that our proposed method achieved higher accuracy and F1 score, without the help of any annotated data which is a significant improvement. We have used two different datasets (Con-SeP dataset, and Glass-contest dataset, both contains Colorectal Cancer histopathology images) to check the effectiveness and validity of our proposed method. These results have shown that our proposed method outperformed other image processing or unsupervised methods both qualitatively and quantitatively.

Automated nuclei segmentation and classification are the keys to analyze and understand the cellular characteristics and functionality, supporting computer-aided digital pathology in disease diagnosis. However, the task still remains challenging due to the intrinsic variations in size, intensity, and morphology of different types of nuclei. Herein, we propose a self-guided ordinal regression neural network for simultaneous nuclear segmentation and classification that can exploit the intrinsic characteristics of nuclei and focus on highly uncertain areas during training. The proposed network formulates nuclei segmentation as an ordinal regression learning by introducing a distance decreasing discretization strategy, which stratifies nuclei in a way that inner regions forming a regular shape of nuclei are separated from outer regions forming an irregular shape. It also adopts a self-guided training strategy to adaptively adjust the weights associated with nuclear pixels, depending on the difficulty of the pixels that is assessed by the network itself. To evaluate the performance of the proposed network, we employ large-scale multi-tissue datasets with 276349 exhaustively annotated nuclei. We show that the proposed network achieves the state-of-the-art performance in both nuclei segmentation and classification in comparison to several methods that are recently developed for segmentation and/or classification.

Nucleus segmentation and classification are crucial in pathology image analysis. Automated nuclear classification and segmentation methods support analysis and understanding of cell characteristics and functions, and allow the analysis of large-scale nuclear forms in the diagnosis and treatment of diseases. Common problems in these tasks arise from the inconsistent sizes and shapes of the cells in each pathology image. This study aims to develop a new method to address these problems based primarily on the horizontal and vertical distance network (HoVer-Net), multiple filter units, and attention gate mechanisms. The results of the study will significantly impact cell segmentation and classification by showing that a multiple filter unit improves the performance of the original HoVer-Net model. In addition, our experimental results show that the Mulvernet achieves outperforming results in both nuclei segmentation and classification compared to several methods. The ability to segment and classify different types of nuclei automatically has a direct influence on further pathological analysis, offering great potential not only to accelerate the diagnostic process in clinics but also for enhancing our understanding of tissue and cell properties to improve patient care and management.

Nuclei segmentation is a fundamental upstream task of digital pathology image analysis. Existing nuclei segmentation methods usually require pixel-level labeled images from experienced pathologists. In this paper, we proposed an innovative data augmentation workflow for histopathology images: a) generates a set of initial central points randomly with existing human-annotated histopathology image datasets; b) generates nuclei segmentation masks based on the generated centroid points of step a); c) generates Haematoxylin and Eosin (H&E)-stained histopathology images corresponding to the generated nuclei masks. In addition, we proposed a deep attention feature fusion generative adversarial network (DAFF -GAN) to improve the image quality and the photorealism of the generated image. We conducted extensive experiments on several existing nuclei segmentation methods, comparing using raw data with the augmented data by our strategy. Extensive experiments proved the effectiveness of our proposed strategy.

Pine wilt disease (PWD) is the most dangerous biohazard of pine species and poses a serious threat to forest resources. Coupling satellite remote sensing technology and deep learning technology for the accurate monitoring of PWD is an important tool for the efficient prevention and control of PWD. We used Gaofen-2 remote sensing images to construct a dataset of discolored standing tree samples of PWD and selected three semantic segmentation models—DeepLabv3+, HRNet, and DANet—for training and to compare their performance. To build a GAN-based semi-supervised semantic segmentation model for semi-supervised learning training, the best model was chosen as the generator of generative adversarial networks (GANs). The model was then optimized for structural adjustment and hyperparameter adjustment. Aimed at the characteristics of Gaofen-2 images and discolored standing trees with PWD, this paper adopts three strategies—swelling prediction, raster vectorization, and forest floor mask extraction—to optimize the image identification process and results and conducts an application demonstration study in Nanping city, Fujian Province. The results show that among the three semantic segmentation models, HRNet was the optimal conventional semantic segmentation model for identifying discolored standing trees of PWD based on Gaofen-2 images and that its MIoU value was 68.36%. Additionally, the GAN-based semi-supervised semantic segmentation model GAN_HRNet_Semi improved the MIoU value by 3.10%, and its recognition segmentation accuracy was better than the traditional semantic segmentation model. The recall rate of PWD discolored standing tree monitoring in the demonstration area reached 80.09%. The combination of semi-supervised semantic segmentation technology and high-resolution satellite remote sensing technology provides new technical methods for the accurate wide-scale monitoring, prevention, and control of PWD.

A Deep Learning Approach for Histology-Based Nucleus Segmentation and Tumor Microenvironment Characterization

As an important link between human and nature, land use/land cover change (LUCC) has become a research hotspot since the first day of the issue initiated. Remote sensing observation supplies important data source for LUCC research. With the constant improvement of the remote sensed image spatial resolution and the continuous development of computer scientific algorithms and models, the study of semantic segmentation in the field of automatic interpretation of remote sensed images has promoted quickly. There have been a number of achievements focusing on the one-class extraction of LUCC classification system, but limited progress in multi-class classifying mission when facing high resolution remote sensing data by using semantic segmentation model, because of its sophisticated structure, the phenomenon of synonyms spectrum and foreign body with spectrum in images. Additionally, the limitation of the semantic segmentation model is a crucial issue which needs to be solv for precision of classification in class recognition and the perfection of semantic segmentation on pixel level as well. The High-Resolution network (HRnet) model was used and improved in the study for semantic segmentation because it has the advantage of low resolution loss. In the LUCC classification work, the distribution of classes (such as cultivated land, woodland, grassland, other land, water, etc.) are usually extremely imbalanced, that leads to the limited classification recognition results of land types when using HRnet. So a combined Loss function of Lovasz Softmax Loss+Cross Entropy Loss was used in HRnet to classify the land cover of remote sensing images, to meet the requirements of high-resolution image classification not only in terms of low resolution loss but also in terms of class recognition. The combined loss function provided the direction of the model, and the appropriate loss function improved the performance of the model when faced with the imbalanced distribution of land classes. The results are as follows: 1) Compared with Deeplab and Unet, HRnet model performed better in segmentation results; 2) HRnet model with combined Loss function Lovasz Softmax Loss+Cross Entropy Loss (HRnet+) had better performance, and its test accuracy PA(Pixel Accuracy) value was 0.9577, MIOU (Mean Intersection over Union) value was 0.8801, and Kappa value was 0.9455. This indicated that the HRnet model with low loss of resolution could achieve better results in the automatic segmentation of high-resolution remote sensing images, and the combined loss function constructed in this study could effectively solve the problem of imbalanced distribution of classes in remote sensing images, and the edge optimization ability was also more significant.

Semantic segmentation of weed and crop images is a key component and prerequisite for automated weed management. For weeds in unmanned aerial vehicle (UAV) images, which are usually characterized by small size and easily confused with crops at early growth stages, existing semantic segmentation models have difficulties to extract sufficiently fine features. This leads to their limited performance in weed and crop segmentation of UAV images. We proposed a fine-grained feature-guided UNet, named FG-UNet, for weed and crop segmentation in UAV images. Specifically, there are two branches in FG-UNet, namely the fine-grained feature branch and the UNet branch. In the fine-grained feature branch, a fine feature-aware (FFA) module was designed to mine fine features in order to enhance the model's ability to segment small objects. In the UNet branch, we used an encoder-decoder structure to realize high-level semantic feature extraction in images. In addition, a contextual feature fusion (CFF) module was designed for the fusion of the fine features and high-level semantic features, thus enhancing the feature discrimination capability of the model. The experimental results showed that our proposed FG-UNet, achieved state-of-the-art performance compared to other semantic segmentation models, with mean intersection over union (MIOU) and mean pixel accuracy (MPA) of 88.06% and 92.37%, respectively. The proposed method in this study lays a solid foundation for accurate detection and intelligent management of weeds. It will have a positive impact on the development of smart agriculture. © 2024 Society of Chemical Industry.

A nuclei segmentation in the histopathological images is a challenging problem, specifically in the images stained with the hematoxylin and eosin dye. To alleviate this, a new whale optimization algorithm based fuzzy clustering method has been presented in this work for nuclei segmentation in the histopathological images. In the proposed method, the whale optimization algorithm is applied to find the best fuzzy clusters based on the objective function defined as compactness. The evaluation of the introduced method is conducted on the publicly available histopathological image dataset, namely H&E stained ER+ breast cancer images. The experimental results evince that the proposed approach acquires comparatively better accuracy of segmentation than the standard clustering based image segmentation methods in terms of both the qualitative and quantitative measurements. Therefore, it can be stated that the introduced method is an efficacious nuclei segmentation method for histopathological images.

Nucleus segmentation in histopathology images holds great clinical value for disease analysis. With the advancements in deep learning and continuous iteration of devices, existing nucleus segmentation algorithms can achieve satisfactory performance. However, these fully supervised nucleus segmentation methods require pixel-level annotation information, which requires a significant amount of time and effort. To ease this burden of annotations, we propose an envelope enhancement segmentation Network (EESNet) for weak supervison nucleus segmentation. Specifically, we first employ a Voronoi diagram and adaptive k-means clustering algorithm to derive two kinds of informative pixel-level pseudo labels,which are used for pixel-wise segmentation. Furthermore, we introduce an envelope enhancement network to provide rich envelope structure information to the segmentation network, which helps mitigate the problem of inaccurate boundary segmentation caused by point annotations. Finally, our network is verified on a mainstream nucleus segmentation datasets (consep) and achieves satisfactory performance.

Oral epithelial dysplasia (OED) is a pre-cancerous histopathological diagnosis given to a range of oral lesions. Architectural, cytological and histological features of OED can be modelled through the segmentation of full epithelium, individual nuclei and stroma (connective tissues) to provide significant diagnostic features. In this paper, we explore a customised neural architecture search (NAS) based method for optimisation of an efficient architecture for segmentation of the full epithelium and individual nuclei in pathology whole slide images (WSIs). Our initial experimental results show that the NAS-derived architecture achieves 93.5% F1-score for the full epithelium segmentation and 94.5% for nuclear segmentation outperforming other state-of-the-art models. Accurate nuclear segmentation allows us to perform quantitative statistical and morphometric feature analyses of the segmented nuclei within regions of interest (ROIs) of multi-gigapixel whole-slide images (WSIs). We show that a random forest model using these features can differentiate between low-risk and high-risk OED lesions.KeywordsOral epithelial dysplasiaComputational pathologyNeural architecture searchDigital pathologyDeep learningMachine learning

Chapter Thirteen - Toward large-scale histopathological image analysis via deep learning