A Nuclei Segmentation Method Based on Whale Optimization Algorithm Fuzzy Clustering in Histopathological Images

In automatic cancer detection, nuclei segmentation is a very essential step which enables the classification task simpler and computationally more efficient. However, automatic nuclei detection is fraught with the problems of inter-class variability of nuclei size and shapes. In this research article, a novel unsupervised edge detection technique, is proposed for segmenting the nuclei regions in liver cancer Hematoxylin and Eosin (H&E) stained histopathology images. In this novel edge detection technique, the notion of computing local standard deviation is incorporated, instead of computing gradients. Since, local standard deviation value is correlated with the edge information of image, this novel method can extract the nuclei edges efficiently, even at multiscale. The edge-detected image is further converted into a binary image by employing Ostu (IEEE Trans Syst Man Cybern 9(1):62–66, 1979)’s thresholding operation. Subsequently, an adaptive morphological filter is also employed in order to refine the final segmented image. The proposed nuclei segmentation method is also tested on a well-recognized multi-organ dataset, in order to check its effectiveness over wide variety of dataset. The visual results of both datasets indicate that the proposed segmentation method overcomes the limitations of existing unsupervised methods, moreover, its performance is comparable with the same of recent deep neural models like DIST, HoverNet, etc. Furthermore, three quality metrics are computed in order to measure the performance of several nuclei segmentation methods quantitatively. The mean value of quality metrics reveals that proposed segmentation method indeed outperformed other existing nuclei segmentation methods.

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.

Circular shape constrained fuzzy clustering (CiscFC) for nucleus segmentation in Pap smear 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.

This paper presents a method for automatic segmentation of nuclei in phase-contrast images using the intensity, convexity and texture of the nuclei. The proposed method consists of three main stages: preprocessing, h-maxima transformation-based marker controlled watershed segmentation ( h-TMC), and texture analysis. In the preprocessing stage, a top-hat filter is used to increase the contrast and suppress the non-uniform illumination, shading, and other imaging artifacts in the input image. The nuclei segmentation stage consists of a distance transformation, h-maxima transformation and watershed segmentation. These transformations utilize the intensity information and the convexity property of the nucleus for the purpose of detecting a single marker in every nucleus; these markers are then used in the h-TMC watershed algorithm to obtain segments of the nuclei. However, dust particles, imaging artifacts, or prolonged cell cytoplasm may falsely be segmented as nuclei at this stage, and thus may lead to an inaccurate analysis of the cell image. In order to identify and remove these non-nuclei segments, in the third stage a texture analysis is performed, that uses six of the Haralick measures along with the AdaBoost algorithm. The novelty of the proposed method is that it introduces a systematic framework that utilizes intensity, convexity, and texture information to achieve a high accuracy for automatic segmentation of nuclei in the phase-contrast images. Extensive experiments are performed demonstrating the superior performance ( precision = 0.948; recall = 0.924; F1-measure = 0.936; validation based on ∼4850 manually-labeled nuclei) of the proposed method.

Detecting and segmenting cell nuclei in two-dimensional microscopy images

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.

BackgroundHistopathology image analysis is a gold standard for cancer recognition and diagnosis. Automatic analysis of histopathology images can help pathologists diagnose tumor and cancer subtypes, alleviating the workload of pathologists. There are two basic types of tasks in digital histopathology image analysis: image classification and image segmentation. Typical problems with histopathology images that hamper automatic analysis include complex clinical representations, limited quantities of training images in a dataset, and the extremely large size of singular images (usually up to gigapixels). The property of extremely large size for a single image also makes a histopathology image dataset be considered large-scale, even if the number of images in the dataset is limited.ResultsIn this paper, we propose leveraging deep convolutional neural network (CNN) activation features to perform classification, segmentation and visualization in large-scale tissue histopathology images. Our framework transfers features extracted from CNNs trained by a large natural image database, ImageNet, to histopathology images. We also explore the characteristics of CNN features by visualizing the response of individual neuron components in the last hidden layer. Some of these characteristics reveal biological insights that have been verified by pathologists. According to our experiments, the framework proposed has shown state-of-the-art performance on a brain tumor dataset from the MICCAI 2014 Brain Tumor Digital Pathology Challenge and a colon cancer histopathology image dataset.ConclusionsThe framework proposed is a simple, efficient and effective system for histopathology image automatic analysis. We successfully transfer ImageNet knowledge as deep convolutional activation features to the classification and segmentation of histopathology images with little training data. CNN features are significantly more powerful than expert-designed features.

Due to the complexity of histopathology tissues, an accurate classification and segmentation of cancer diagnosis is a challenging task in computer vision. The nuclei segmentation of microscopic images is a key prerequisite for cancerous pathological image analysis. However, an accurate nuclei segmentation is a long running major challenge due to the enormous color variability of staining, nuclei shapes, sizes, and clustering of overlapping cells. To address these challenges and early diagnosis as well as reduce the bias decisions of expert lab technician of cancer in clinical practice, the authors study the classification of computer-aided frameworks and automatic nuclei segmentation frameworks based on histopathology images by convolutional deep learning. The authors have used a publicly available PatchCamelyon and 2018 Data Science Bowl histology image dataset for this study. The results are compared and expected to be useful clinically for technician experts in the analysis of cancer diagnosis and the survival chances of patients.

Multilevel thresholding is an effective and indispensable technology for image segmentation that has attracted extensive attention in recent years. However, the multilevel thresholding method has some disadvantages, such as a large computational complexity and low segmentation accuracy. Therefore, this paper proposes a whale optimization algorithm (WOA) based on Kapur's entropy method to solve the image segmentation problem. The WOA can effectively balance exploration and exploitation to avoid falling into premature convergence and obtain the global optimal solution. To verify the segmentation performance of the WOA, a series of experiments on underwater images from the experimental pool of Harbin Engineering University are conducted, and the segmentation results are compared with those of the BA, the FPA, MFO, the MSA, PSO and WWO by maximizing the fitness value of Kapur's entropy method. The fitness value, peak signal-to-noise ratio (PSNR), structure similarity index (SSIM), execution time and Wilcoxon's rank-sum test are used to evaluate the overall performance of each algorithm. The experimental results reveal that the WOA is superior to the other comparison algorithms and has a higher segmentation accuracy, better segmentation effect and stronger robustness. In addition, the feasibility and efficiency of the WOA are verified.

Automated cell nuclei segmentation is the most crucial step toward the implementation of a computer-aided diagnosis system for cancer cells. Studies on the automated analysis of cytology pleural effusion images are few because of the lack of reliable cell nuclei segmentation methods. Therefore, this paper presents a comparative study of twelve nuclei segmentation methods for cytology pleural effusion images. Each method involves three main steps: preprocessing, segmentation, and postprocessing. The preprocessing and segmentation stages help enhancing the image quality and extracting the nuclei regions from the rest of the image, respectively. The postprocessing stage helps in refining the segmented nuclei and removing false findings. The segmentation methods are quantitatively evaluated for 35 cytology images of pleural effusion by computing five performance metrics. The evaluation results show that the segmentation performances of the Otsu, k-means, mean shift, Chan–Vese, and graph cut methods are 94, 94, 95, 94, and 93%, respectively, with high abnormal nuclei detection rates. The average computational times per image are 1.08, 36.62, 50.18, 330, and 44.03 seconds, respectively. The findings of this study will be useful for current and potential future studies on cytology images of pleural effusion.

Recently, artificial intelligence (AI) is an extremely revolutionized domain of medical image processing. Specifically, image segmentation is a task that generally aids in such an improvement. This boost performs great developments in the conversion of AI approaches in the research lab to real medical applications, particularly for computer-aided diagnosis (CAD) and image-guided operation. Mitotic nuclei estimates in breast cancer instances have a prognostic impact on diagnosis of cancer aggressiveness and grading methods. The automated analysis of mitotic nuclei is difficult due to its high similarity with nonmitotic nuclei and heteromorphic form. This study designs an artificial hummingbird algorithm with transfer-learning-based mitotic nuclei classification (AHBATL-MNC) on histopathologic breast cancer images. The goal of the AHBATL-MNC technique lies in the identification of mitotic and nonmitotic nuclei on histopathology images (HIs). For HI segmentation process, the PSPNet model is utilized to identify the candidate mitotic patches. Next, the residual network (ResNet) model is employed as feature extractor, and extreme gradient boosting (XGBoost) model is applied as a classifier. To enhance the classification performance, the parameter tuning of the XGBoost model takes place by making use of the AHBA approach. The simulation values of the AHBATL-MNC system are tested on medical imaging datasets and the outcomes are investigated in distinct measures. The simulation values demonstrate the enhanced outcomes of the AHBATL-MNC method compared to other current approaches.

Quantification of phenotypes in high-content screening experiments depends on the accuracy of single cell analysis. In such analysis workflows, cell nuclei segmentation is typically the first step and is followed by cell body segmentation, feature extraction, and subsequent data analysis workflows. Therefore, it is of utmost importance that the first steps of high-content analysis are done accurately in order to guarantee correctness of the final analysis results. In this paper, we present a novel cell nuclei image segmentation framework which exploits robustness of graph cut to obtain initial segmentation for image intensity-based clump splitting method to deliver the accurate overall segmentation. By using quantitative benchmarks and qualitative comparison with real images from high-content screening experiments with complicated multinucleate cells, we show that our method outperforms other state-of-the-art nuclei segmentation methods. Moreover, we provide a modular and easy-to-use implementation of the method for a widely used platform.

Automatic recognition of histopathological image plays an important role in building computer-aid diagnosis system. Traditionally hand-craft features are widely used for representing histopathological images when building recognition models. Currently with the development of deep learning algorithms, deep features obtained directly from pre-trained networks at less costs show that they perform better than traditional ones. However, most recent work adopts common pre-trained networks for feature extraction and train a classifier with domain knowledge which generates a gap between the common extracted features and the application domain. To fill the gap and improve the performance of the recognition model, in this paper we propose a deep model for histopathological image feature representation in a supervised-learning manner. The proposed model is constructed based on some pre-trained convolutional neural networks. After supervised learning, the feature learning network captures most domain knowledge. The proposed model is evaluated on two histopathological image datasets and the results show that the proposed model is superior to current state-of-the-art models.

Modified hybrid bat algorithm with genetic crossover operation and smart inertia weight for multilevel image segmentation