Segmentation Of Cell Nuclei Research Articles

Enhancing Multi-tissue and Multi-scale Cell Nuclei Segmentation with Deep Metric Learning

(1) Background: The segmentation of cell nuclei is an essential task in a wide range of biomedical studies and clinical practices. The full automation of this process remains a challenge due to intra- and internuclear variations across a wide range of tissue morphologies, differences in staining protocols and imaging procedures. (2) Methods: A deep learning model with metric embeddings such as contrastive loss and triplet loss with semi-hard negative mining is proposed in order to accurately segment cell nuclei in a diverse set of microscopy images. The effectiveness of the proposed model was tested on a large-scale multi-tissue collection of microscopy image sets. (3) Results: The use of deep metric learning increased the overall segmentation prediction by 3.12% in the average value of Dice similarity coefficients as compared to no metric learning. In particular, the largest gain was observed for segmenting cell nuclei in H&E -stained images when deep learning network and triplet loss with semi-hard negative mining were considered for the task. (4) Conclusion: We conclude that deep metric learning gives an additional boost to the overall learning process and consequently improves the segmentation performance. Notably, the improvement ranges approximately between 0.13% and 22.31% for different types of images in the terms of Dice coefficients when compared to no metric deep learning.

Microscopy cell nuclei segmentation with enhanced U-Net

BackgroundCell nuclei segmentation is a fundamental task in microscopy image analysis, based on which multiple biological related analysis can be performed. Although deep learning (DL) based techniques have achieved state-of-the-art performances in image segmentation tasks, these methods are usually complex and require support of powerful computing resources. In addition, it is impractical to allocate advanced computing resources to each dark- or bright-field microscopy, which is widely employed in vast clinical institutions, considering the cost of medical exams. Thus, it is essential to develop accurate DL based segmentation algorithms working with resources-constraint computing.ResultsAn enhanced, light-weighted U-Net (called U-Net+) with modified encoded branch is proposed to potentially work with low-resources computing. Through strictly controlled experiments, the average IOU and precision of U-Net+ predictions are confirmed to outperform other prevalent competing methods with 1.0% to 3.0% gain on the first stage test set of 2018 Kaggle Data Science Bowl cell nuclei segmentation contest with shorter inference time.ConclusionsOur results preliminarily demonstrate the potential of proposed U-Net+ in correctly spotting microscopy cell nuclei with resources-constraint computing.

An efficient algorithm for detection of white blood cell nuclei using adaptive three stage PCA-based fusion

Abstract Morphological analysis of white blood cells under a microscope is a crucial laboratory procedure for the diagnosis of several diseases including leukemia. This process is however, tedious and subjective, hence the need for innovative, efficient, and automatic analytical techniques. From shortcomings of algorithms in the literature such as inability to segment images with poor brightness and low contrast or deterioration of morphological structure of nucleus during segmentation, this paper sets forth an automatic method for segmentation of white blood cell nuclei in peripheral blood smear images in an attempt to cover these defects. In the proposed method, an adaptive fusion based on principal components analysis is used to fuse color components derived from HSV and CMYK color spaces. The proposed method enables the extraction of the nuclei without the application of morphological operations and presents the advantage of accentuated contrast thanks to PCA-based fusion and independence to color and brightness variation in the peripheral images. The developed algorithm was tested on three completely different public image datasets. The comparison of the results of the proposed algorithm with several other existing methods on the same datasets demonstrated its greater efficacy. A dice similarity coefficient of 97.06% was obtained for CellaVision, 94.75% for BloodSeg base, and 90.79% for JTSC databases.

Automated oral squamous cell carcinoma identification using shape, texture and color features of whole image strips

Despite profound knowledge of the incidence of oral cancers and a large body of research beyond it, it continues to beat diagnosis and treatment management. Post physical observation by clinicians, a biopsy is a gold standard for accurate detection of any abnormalities. Towards the application of artificial intelligence as an aid to diagnosis, automated cell nuclei segmentation is the most essential step for the recognition of the cancer cells. In this study, we have extracted the shape, texture and color features from the histopathological images collected indigenously from regional hospitals. A dataset of 42 whole slide slices was used to automatically segment and generate a cell level dataset of 720 nuclei. Next, different classifiers were applied for classification purposes. 99.4 % accuracy using Decision Tree Classifier, 100 % accuracy using both SVM and Logistic regression and 100 % accuracy using SVM, Logistic regression and Linear Discriminant were acquired for shape, textural and color features respectively. The in-depth analysis showed SVM and Linear Discriminant classifier gave the best result for texture and color features respectively. The achieved result can be effectively converted to software as an assistant diagnostic tool.

An ensemble of fine-tuned fully convolutional neural networks for pleural effusion cell nuclei segmentation

Pleural effusion (PE) is a problem commonly encountered in patients with malignant neoplasms, especially carcinomas of the breast and lung. Nuclei segmentation is a prerequisite step of a computer-aided diagnosis (CAD) system for pleural cancer. We propose an ensemble of fully convolutional neural networks (FCNN) for PE cell nuclei segmentation. A two-stage method, fine-tuning of deep FCNN and an ensemble network, is designed. It involves, first, fine-tuning the well-known deep learning-based segmentation networks such as fully convolutional network (FCN), SegNet, and U-Net, and then employing an ensemble network that uses the features from fine-tuned networks to improve the efficiency. The proposed ensemble method achieves a Jaccard index of 90.82%, a sensitivity of 97.15%, and a specificity of 99.80% on the new dataset consisting of 120 PE cytology images. These experimental results have not only contributed to the pleural cancer diagnosis but also demonstrated the effectiveness of an ensemble of FCNN.

Automated acute lymphoblastic leukaemia detection system using microscopic images

An automatic and novel approach for acute lymphoblastic leukaemia classification is proposed. The proposed scheme is based on pre-processing and segmentation of white blood cell nuclei using expectation maximisation algorithm, feature extraction, feature selection using principal component analysis and classification using sparse representation. The accuracy of the proposed scheme significantly outperforms the existing schemes in terms of acute lymphoblastic leukaemia classification.

A segmentation method combining probability map and boundary based on multiple fully convolutional networks and repetitive training

Cell nuclei image segmentation technology can help researchers observe each cell’s stress response to drug treatment. However, it is still a challenge to accurately segment the adherent cell nuclei. At present, image segmentation based on a fully convolutional network (FCN) is attracting researchers’ attention. We propose a multiple FCN architecture and repetitive training (M-FCN-RT) method to learn features of cell nucleus images. In M-FCN-RT, the multiple FCN (M-FCN) architecture is composed of several single FCNs (S-FCNs) with the same structure, and each FCN is used to learn the specific features of image datasets. In this paper, the M-FCN contains three FCNs; FCN1-2, FCN3 and FCNB. FCN1-2 and FCN3 are respectively used to learn the spatial features of cell nuclei for generating probability maps to indicate nucleus regions of an image; FCNB (boundary FCN) is used to learn the edge features of cell nuclei for generating the nucleus boundary. For the training of each FCN, we propose a repetitive training (RT) method to improve the classification accuracy of the model. To segment cell nuclei, we finally propose an algorithm combining the probability map and boundary (PMB) to segment the adherent nuclei. This paper uses a public opening nucleus image dataset to train, verify and evaluate the proposed M-FCN-RT and PMB methods. Our M-FCN-RT method achieves a high Dice similarity coefficient (DSC) of 92.11%, 95.64% and 87.99% on the three types of sub-datasets respectively for probability maps. In addition, segmentation experimental results show the PMB method is more effective and efficient compared with other methods.

An Effective Encoder-Decoder Network for Neural Cell Bodies and Cell Nucleus Segmentation of EM Images.

Neural systems are complicated networks connected by a large number of neurons through gap junctions and synapse. At present, for electron microscopy connectomics research, neuron structure recognition algorithms mostly focus on synapses, dendrites, axons and mitochondria, etc. However, effective methods for automatic recognition of neuronal cell bodies are rare. In this paper, we proposed an effective encoderdecoder network, which extracted segmentation features of neural cell bodies and cell nucleus by the modified residual network and pyramid module. The framework is capable of merging multi-scale contextual information and generating efficient segmentation results by integrating multilevel features. We applied this proposed network on two segmentation tasks for electron microscope (EM) images and compared it with other promising methods as U-Net and deeplab v3+. The results demonstrated that our method achieved the state-of-the-art performance on quality metrics. Finally, we visualized two intact neural cell bodies and cell nucleus to provide a close look into these fine structures.

Cell Nuclei Segmentation in Cytological Images Using Convolutional Neural Network and Seeded Watershed Algorithm

Morphometric analysis of nuclei is crucial in cytological examinations. Unfortunately, nuclei segmentation presents many challenges because they usually create complex clusters in cytological samples. To deal with this problem, we are proposing an approach, which combines convolutional neural network and watershed transform to segment nuclei in cytological images of breast cancer. The method initially is preprocessing images using color deconvolution to highlight hematoxylin-stained objects (nuclei). Next, convolutional neural network is applied to perform semantic segmentation of preprocessed image. It finds nuclei areas, cytoplasm areas, edges of nuclei, and background. All connected components in the binary mask of nuclei are treated as potential nuclei. However, some objects actually are clusters of overlapping nuclei. They are detected by their outlying values of morphometric features. Then an attempt is made to separate them using the seeded watershed segmentation. If the attempt is successful, they are included in the nuclei set. The accuracy of this approach is evaluated with the help of referenced, manually segmented images. The degree of matching between reference nuclei and discovered objects is measured with the help of Jaccard distance and Hausdorff distance. As part of the study, we verified how the use of a convolutional neural network instead of the intensity thresholding to generate a topographical map for the watershed improves segmentation outcomes. Our results show that convolutional neural network outperforms Otsu thresholding and adaptive thresholding in most cases, especially in scenarios with many overlapping nuclei.

Comparative analysis of nucleus segmentation techniques for malignancy detection of pap smear cervical cells

Pap smear is a microscopic screening process of cervical smear used to detect pre-cancerous and cancerous cells in the cervix region. Cell nuclei segmentation is one of the most significant task in cervical cell image analysis which aids in identifyi

Automated Segmentation of Fluorescence Microscopy Images for 3D Cell Detection in human-derived Cardiospheres

The ‘cardiosphere’ is a 3D cluster of cardiac progenitor cells recapitulating a stem cell niche-like microenvironment with a potential for disease and regeneration modelling of the failing human myocardium. In this multicellular 3D context, it is extremely important to decrypt the spatial distribution of cell markers for dissecting the evolution of cellular phenotypes by direct quantification of fluorescent signals in confocal microscopy. In this study, we present a fully automated method, named CARE (‘CARdiosphere Evaluation’), for the segmentation of membranes and cell nuclei in human-derived cardiospheres. The proposed method is tested on twenty 3D-stacks of cardiospheres, for a total of 1160 images. Automatic results are compared with manual annotations and two open-source software designed for fluorescence microscopy. CARE performance was excellent in cardiospheres membrane segmentation and, in cell nuclei detection, the algorithm achieved the same performance as two expert operators. To the best of our knowledge, CARE is the first fully automated algorithm for segmentation inside in vitro 3D cell spheroids, including cardiospheres. The proposed approach will provide, in the future, automated quantitative analysis of markers distribution within the cardiac niche-like environment, enabling predictive associations between cell mechanical stresses and dynamic phenotypic changes.

Binary tree-like network with two-path Fusion Attention Feature for cervical cell nucleus segmentation

Early detection of cervical lesion is of great significance in reducing mortality from cervical cancer, and segmentation of cervical cell nuclei plays an important role in screening for cervical lesion. Compared with traditional algorithms, several deep learning methods can improve the segmentation; however, due to blurred boundaries and complex gradients of medical images, the segmentation remains unsatisfactory. In addition, the existing datasets used by cervical cell nucleus segmentation research are lacking in terms of both quantity and diversity, so methods based on those datasets cannot effectively cope with challenging cases. This paper releases a new cervical cell dataset and proposes a network named Binary Tree-like Network with Two-path Fusion Attention Feature (BTTFA). The simplified diagram of BTTFA is similar to a binary tree structure and combines ResNeXt's last four layers of information by integrating adjacent pairs of layers each time; therefore, the information of multilayers can be fully integrated, and the information lost by the pooling layers can be recovered. BTTFA also applies a two-path fusion attention to selectively utilize information close to the root nodes, thereby taking full advantage of low-level detail and high-level semantic information and selectively emphasizing important features while suppressing less useful ones. Meanwhile, at some nodes of the binary tree-like network, focal loss is imposed to calculate the loss between the ground truth and the feature map during the training process. Experiments demonstrate that BTTFA performs better than the existing technology on our dataset and another public dataset.

Segmentation of Heavily Clustered Nuclei from Histopathological Images

Automated cell nucleus segmentation is the key to gain further insight into cell features and functionality which support computer-aided pathology in early diagnosis of diseases such as breast cancer and brain tumour. Despite considerable advances in automated segmentation, it still remains a challenging task to split heavily clustered nuclei due to intensity variations caused by noise and uneven absorption of stains. To address this problem, we propose a novel method applicable to variety of histopathological images stained for different proteins, with high speed, accuracy and level of automation. Our algorithm is initiated by applying a new locally adaptive thresholding method on watershed regions. Followed by a new splitting technique based on multilevel thresholding and the watershed algorithm to separate clustered nuclei. Finalized by a model-based merging step to eliminate oversegmentation and a model-based correction step to improve segmentation results and eliminate small objects. We have applied our method to three image datasets: breast cancer stained for hematoxylin and eosin (H&E), Drosophila Kc167 cells stained for DNA to label nuclei, and mature neurons stained for NeuN. Evaluated results show our method outperforms the state-of-the-art methods in terms of accuracy, precision, F1-measure, and computational time.

Segmentation of Nuclei in Histopathology Images by Deep Regression of the Distance Map

The advent of digital pathology provides us with the challenging opportunity to automatically analyze whole slides of diseased tissue in order to derive quantitative profiles that can be used for diagnosis and prognosis tasks. In particular, for the development of interpretable models, the detection and segmentation of cell nuclei is of the utmost importance. In this paper, we describe a new method to automatically segment nuclei from Haematoxylin and Eosin (H&E) stained histopathology data with fully convolutional networks. In particular, we address the problem of segmenting touching nuclei by formulating the segmentation problem as a regression task of the distance map. We demonstrate superior performance of this approach as compared to other approaches using Convolutional Neural Networks.

An Accurate Nuclei Segmentation Algorithm in Pathological Image Based on Deep Semantic Network

Cell (nuclei) segmentation is the basic and key step of pathological image analysis. However, robust and accurate cell (nuclei) segmentation is a difficult problem due to the enormous variability of staining, cell sizes, morphologies and cell adhesion or overlapping. In this paper, we extend U-Net with atrous depthwise separable convolution (AS-UNet) for cell (nuclei) segmentation. AS-UNet consists of three parts: encoder module, decoder module and atrous convolution module. The encoder module obtains the high-level semantic information of the cell image layer by layer, while the decoder module gradually recovers the spatial information. The atrous convolution module is composed of cascade and parallel atrous convolution operations. It can extract and combine multi-scale features so that the model can get strong perception ability for both small and large cells. At the same time, the atrous convolution can significantly increase the receptive field of the network model without hurting the segmentation performance or increasing the computational cost. During the training period, Log-Dice loss and Focal loss are combined, while Adam optimization method is employed to optimize the network. In order to increase the penalty for the smaller prediction result of the Dice coefficient, which is carried out by logarithmic operation and the negative value is taken as the Log-Dice loss. The above optimization is beneficial for the convergence speed. Additionally, some data augmentation techniques are applied to increase online data, which contribute to improving the robustness of the model. Compared with several state-of-the-art semantic segmentation algorithms, our method achieves the promising performance on two latest released pathological image datasets.

Deep-Learning-Based Label-Free Segmentation of Cell Nuclei in Time-Lapse Refractive Index Tomograms

We proposed a method of label-free segmentation of cell nuclei by exploiting a deep learning (DL) framework. Over the years, fluorescent proteins and staining agents have been widely used to identify cell nuclei. However, the use of exogenous agents inevitably prevents from long-term imaging of live cells and rapid analysis and even interferes with intrinsic physiological conditions. Without any agents, the proposed method was applied to label-free optical diffraction tomography (ODT) of human breast cancer cells. A novel architecture with optimized training strategies was validated through cross-modality and cross-laboratory experiments. The nucleus volumes from the DL-based label-free ODT segmentation accurately agreed with those from fluorescent-based. Furthermore, the 4D cell nucleus segmentation was successfully performed for the time-lapse ODT images. The proposed method would bring out broad and immediate biomedical applications with our framework publicly available.

Contour-Aware Residual W-Net for Nuclei Segmentation

Nuclei segmentation is an important pre-processing step for any vision based cytopathological diagnostic system which extracts information from nuclei to perform tasks such as cancer detection. A cell nuclei segmentation pipeline should be robust, accurate and fast. We propose a deep learning based model, Contour-Aware Residual W-Net (WRC-Net), which consists of double U-Net, [5] or W-Net. The first U-Net learns to predict nuclei boundaries and the second generates the segmentation map. Our model can accurately segment a 128x128 dimensional image in less than 0.05s. Our model can learn from a very limited training data with as low as a single training image. We tested our model on real HE (Hematoxylin and Eosin) stained cell images and it showed better overall performance against previous state-of-the-art nuclei segmentation methods.

Quality assessment of Ki67 staining using cell line proliferation index and stain intensity features.

Breast cancer is the most frequent cancer among women worldwide. Ki67 can be used as an immunohistochemical pseudo marker for cell proliferation to determine how aggressive the cancer is and thereby the treatment of the patient. No standard Ki67 staining protocol exists, resulting in inter-laboratory stain variability. Therefore, it is important to determine the quality control of a staining protocol to ensure correct diagnosis and treatment of patients. Currently, quality control is performed by the organization NordiQC that use an expert panel-based qualitative assessment system. However, no objective method exists to determine the quality of a staining protocol. In this study, we propose an algorithm, to objectively assess staining quality from segmented cell nuclei structures extracted from cell lines. The cell nuclei were classified into either Ki67 positive or negative to determine the Ki67 proliferation index within the cell lines. A Ki67 stain quality model based on ordinal logistic regression was developed to determine the quality of a staining protocol from features extracted from the segmented cell nuclei in the cell lines. The algorithm was able to segment and classify Ki67 positive cell nuclei with a sensitivity and positive predictive value (PPV) of 0.90 and 0.94 and Ki67 negative cell nuclei with a sensitivity and PPV of 0.78 and 0.78. The mean difference between a manual and automatic Ki67 proliferation index was -0.003 with a standard deviation of 0.056. The ordinal logistic regression model found that the stain intensity for both the Ki67 positive and Ki67 negative cell nuclei were statistically significant as parameters determining the stain quality from the cell line cores. The framework shows great promise for using cell nuclei information from cell lines to predict the staining quality of staining protocols. © 2018 International Society for Advancement of Cytometry.

Mixture Model Segmentation System for Parasagittal Meningioma brain Tumor Classification based on Hybrid Feature Vector.

Meningioma is the one of the most common type of brain tumor, it as arises from the meninges and encloses the spine and the brain inside the skull. It accounts for 30% of all types of brain tumor. Meningioma's can occur in many parts of the brain and accordingly it is named. In this paper, a mixture model based classification of meningioma brain tumor using MRI image is developed. The proposed method consists of four stages. In the first stage, with respect to the cells' boundary, it is necessary to further processing, which ensures the boundary of some cells is a discrete region. Mathematical Morphology brings a fancy result during the discrete processing. Accurate cancer cell nucleus segmentation is necessary for automated cytological image analysis. Thresholding is a crucial step in segmentation..An adaptive binarization technique is an important step for medical image analysis.Finally, a novel hybrid Fuzzy SVM is designed in the classification stage meningioma brain tumor. The tumor classification results of proposed feature extraction with SVM is 74.24%, MM with FSVM is 82.67% and MM with RBF is 62.71% and our proposed method MM with Hybrid SVM is 91.64%.

Automatic cell nuclei segmentation and classification of cervical Pap smear images

Abstract Pathological examination of microscopic image of Pap smear slide remains the main method for cervical cancer diagnosis. The accurate segmentation and classification of images are two important phases of the analysis. Firstly, the Mean-Shift clustering algorithm is applied to obtain regions of interest (ROI) for cell nuclei segmentation. Then the flexible mathematical morphology is applied to split overlapped cell nuclei for better accuracy and robustness. For classification of the images, features based on shape, textural features based on color space and Gabor features are extracted and put together to obtain better classification performance. The optimal feature set is obtained by chain-like agent genetic algorithm (CAGA), P-value and maximum relevance-minimum multicollinearity (MRmMC). The proposed segmentation and classification methods were tested on 362 cervical Pap smear images. Experimental results showed that the cervical cell nuclei can be segmented by the proposed segmentation method with high effective segmentation results (Sensitivity: 94.25%±1.03% and Specificity 93.45%±1.14%). The feature selection method based on CAGA with Gabor features has the highest classification performance for normal, uninvolved and abnormal images (more than 96% accuracy). The proposed method can automatically and effectively segment cell nuclei of microscopic images. From the experimental results, Gabor features and feature selection based on CAGA are apparently helpful for improving the performance of classification.