3D brain tumor segmentation in MRI images based on a modified PSO technique

Three-dimensional (3D) brain tumor segmentation is a clinical requirement for brain tumor diagnosis and radiotherapy planning. This is a challenging task due to variation in type, size, location, and shape of tumors. Several methods such as particle swarm optimization (PSO) algorithm formed a topological relationship for the slices that converts 2D images into 3D magnetic resonance imaging (MRI) images which does not provide accurate results and they depend on the number of input sections, positions, and the shape of the MRI images. In this article, we propose an efficient 3D brain tumor segmentation technique called modified particle swarm optimization. Also, segmentation results are compared with Darwinian particle swarm optimization (DPSO) and fractional-order Darwinian particle swarm optimization (FODPSO) approaches. The experimental results show that our method succeeded 3D segmentation with 97.6% of accuracy rate more efficient if compared with the DPSO and FODPSO methods with 78.1% and 70.21% for the case of T1-C modality.     

Enhancing level set brain tumor segmentation using fuzzy shape prior information and deep learning

Magnetic resonance imaging (MRI) brain tumor segmentation is a crucial task for clinical treatment. However, it is challenging owing to variations in type, size, and location of tumors. In addition, anatomical variation in individuals, intensity non-uniformity, and noises adversely affect brain tumor segmentation. To address these challenges, an automatic region-based brain tumor segmentation approach is presented in this paper which combines fuzzy shape prior term and deep learning. We define a new energy function in which an Adaptively Regularized Kernel-Based Fuzzy C-Means (ARKFCM) Clustering algorithm is utilized for inferring the shape of the tumor to be embedded into the level set method. In this way, some shortcomings of traditional level set methods such as contour leakage and shrinkage have been eliminated. Moreover, a fully automated method is achieved by using U-Net to obtain the initial contour, reducing sensitivity to initial contour selection. The proposed method is validated on the BraTS 2017 benchmark dataset for brain tumor segmentation. Average values of Dice, Jaccard, Sensitivity and specificity are 0.93 ± 0.03, 0.86 ± 0.06, 0.95 ± 0.04, and 0.99 ± 0.003, respectively. Experimental results indicate that the proposed method outperforms the other state-of-the-art methods in brain tumor segmentation.     

Integrated segmentation of brain tumor images for radiotherapy and neurosurgery

Segmentation of brain tumor images is an important task in diagnosis and treatment planning for cancer patients. To achieve this goal with standard clinical acquisition protocols, conventionally, either classification algorithms are applied on multimodal MR images or atlas‐based segmentation is used on a high‐resolution monomodal MR image. These two approaches have been commonly regarded separately. We propose to integrate all the available imaging information into one framework to be able to use the information gained from the tissue classification of the multimodal images to perform a more precise segmentation on the high‐resolution monomodal image by atlas‐based segmentation. For this, we combine a state of the art regularized classification method with an enhanced version of an atlas‐registration approach including multiscale tumor‐growth modeling. This contribution offers the possibility to simultaneously segment subcortical structures in the patient by warping the respective atlas labels, which is important for neurosurgical planning and radiotherapy planning. © 2013 Wiley Periodicals, Inc. Int J Imaging Syst Technol, 23, 59–63, 2013     

Research on the magnetic resonance imaging brain tumor segmentation algorithm based on DO-UNet

With the social and economic development and the improvement of people's living standards, smart medical care is booming, and medical image processing is becoming more and more popular in research, of which brain tumor segmentation is an important branch of medical image processing. However, the manual segmentation method of brain tumors requires a lot of time and effort from the doctor and has a great impact on the treatment of patients. In order to solve this problem, we propose a DO-UNet model for magnetic resonance imaging brain tumor image segmentation based on attention mechanism and multi-scale feature fusion to realize fully automatic segmentation of brain tumors. Firstly, we replace the convolution blocks in the original U-Net model with the residual modules to prevent the gradient disappearing. Secondly, the multi-scale feature fusion is added to the skip connection of U-Net to fuse the low-level features and high-level features more effectively. In addition, in the decoding stage, we add an attention mechanism to increase the weight of effective information and avoid information redundancy. Finally, we replace the traditional convolution in the model with DO-Conv to speed up the network training and improve the segmentation accuracy. In order to evaluate the model, we used the BraTS2018, BraTS2019, and BraTS2020 datasets to train the improved model and validate it online, respectively. Experimental results show that the DO-UNet model can effectively improve the accuracy of brain tumor segmentation and has good segmentation performance.     

Image registration-based brain tumor detection and segmentation using ANFIS classification approach

Abnormal cells in human brain lead to the development of tumors. Manual detection of this tumor region is a time-consuming process. Hence, this paper proposes an efficient and automated computer-aided methodology for brain tumor detection and segmentation using image registration technique and classification approaches. This proposed work consists of the following modules: image registration, contourlet transform, and feature extraction with feature normalization, classification, and segmentation. The extracted features are optimized using genetic algorithm, and then an adaptive neuro-fuzzy inference system classification approach is used to classify the features for the detection and segmentation of tumor regions in brain magnetic resonance imaging. A quantitative analysis is performed to evaluate the proposed methodology for brain tumor detection using sensitivity, specificity, segmentation accuracy, precision, and Dice similarity coefficient.     

Multi-Scale Image Segmentation Model for Fine-Grained Recognition of Zanthoxylum Rust

Zanthoxylum bungeanum Maxim, generally called prickly ash, is widely grown in China. Zanthoxylum rust is the main disease affecting the growth and quality of Zanthoxylum. Traditional method for recognizing the degree of infection of Zanthoxylum rust mainly rely on manual experience. Due to the complex colors and shapes of rust areas, the accuracy of manual recognition is low and difficult to be quantified. In recent years, the application of artificial intelligence technology in the agricultural field has gradually increased. In this paper, based on the DeepLabV2 model, we proposed a Zanthoxylum rust image segmentation model based on the FASPP module and enhanced features of rust areas. This paper constructed a fine-grained Zanthoxylum rust image dataset. In this dataset, the Zanthoxylum rust image was segmented and labeled according to leaves, spore piles, and brown lesions. The experimental results showed that the Zanthoxylum rust image segmentation method proposed in this paper was effective. The segmentation accuracy rates of leaves, spore piles and brown lesions reached 99.66%, 85.16% and 82.47% respectively. MPA reached 91.80%, and MIoU reached 84.99%. At the same time, the proposed image segmentation model also had good efficiency, which can process 22 images per minute. This article provides an intelligent method for efficiently and accurately recognizing the degree of infection of Zanthoxylum rust.     

An improved label fusion approach with sparse patch‐based representation for MRI brain image segmentation

The multi‐atlas patch‐based label fusion (LF) method mainly focuses on the measurement of the patch similarity which is the comparison between the atlas patch and the target patch. To enhance the LF performance, the distribution probability about the target can be used during the LF process. Hence, we consider two LF schemes: in the first scheme, we keep the results of the interpolation so that we can obtain the labels of the atlas with discrete values (between 0 and 1) instead of binary values in the label propagation. In doing so, each atlas can be treated as a probability atlas. Second, we introduce the distribution probability of the tissue (to be segmented) in the sparse patch‐based LF process. Based on the probability of the tissue and sparse patch‐based representation, we propose three different LF methods which are called LF‐Method‐1, LF‐Method‐2, and LF‐Method‐3. In addition, an automated estimation method about the distribution probability of the tissue is also proposed. To evaluate the accuracy of our proposed LF methods, the methods were compared with those of the nonlocal patch‐based LF method (Nonlocal‐PBM), the sparse patch‐based LF method (Sparse‐PBM), majority voting method, similarity and truth estimation for propagated segmentations, and hierarchical multi‐atlas LF with multi‐scale feature representation and label‐specific patch partition (HMAS). Based on our experimental results and quantitative comparison, our methods are promising in the magnetic resonance image segmentation. © 2017 Wiley Periodicals, Inc. Int J Imaging Syst Technol, 27, 23–32, 2017     

Multi‐modal brain tumor image segmentation based on SDAE

Accurate tumor segmentation has the ability to provide doctors with a basis for surgical planning. Moreover, brain tumor segmentation needs to extract different tumor tissues (Edema, tumor, tumor enhancement, and necrosis) from normal tissues which is a big challenge because tumor structures vary considerably across patients in terms of size, extension, and localization. In this article, we evaluate a fully automated method for segmenting brain tumor images from multi‐modal magnetic resonance imaging volumes based on stacked de‐noising auto‐encoders (SDAEs). Specially, we adopted multi‐modality information from T1, T1c, T2, and Flair images, respectively. We extracted gray level patches from different modalities as the input of the SDAE. After trained by the SDAE, the raw network parameters will be obtained, which are adopted as a parameter of the feed forward neural network for classification. A simple post‐processing is implemented by threshold segmentation method to generate a mask to get the final segmentation result. By evaluating the proposed method on the BRATS 2015, it can be proven that our method obtains the better performance than other state‐of‐the‐art counterpart methods. And a preliminary dice score of 0.86 for whole tumor segmentation has been achieved.     

Fully automatic brain tumor extraction and tissue segmentation from multimodal MRI brain images

Segmentation of Brain tumor from the magnetic resonance imaging (MRI) of head scans is an essential requirement for clinical diagnosis since manual segmentation is a fatigue and time‐consuming process. Recent computer‐aided diagnosis systems depend on the development of fully automatic methods to overcome these problems. In the present work, a fully automated algorithm is proposed to extract and segment tumor regions from multimodal magnetic resonance imaging (MMMRI) sequences. The algorithm has three phases: (a) tumor portion extraction, (b) tumor substructure segmentation, and (c) 3D postprocessing. First, the algorithm extracts tumor portion using a set of image processing operations from T2, fluid‐attenuated inversion recovery (FLAIR), and T1C images. Here, the proposed modified fuzzy c means clustering algorithm is used for enhancing the tumor portion extraction process. Then, the substructures of tumor such as edema, enhancing tumor, and necrotic regions are segmented from MMMRI sequences, T2, FLAIR, and T1C using region‐wise set operations in Phase II. Finally, 3D visualization of the segmented tumor and volume estimation is performed as postprocessing in Phase III. The proposed work was experimented on BraTS 2013 dataset. The quantitative analysis is performed using William's Index, Dice, sensitivity, specificity, and accuracy and is compared with 19 state‐of‐the‐art methods. The proposed method yields comparable results as 77%, 53%, and 59% of Dice for complete, core, and enhancing tumor regions, respectively.     

Dual‐pathway DenseNets with fully lateral connections for multimodal brain tumor segmentation

Multimodal medical image data provide different structured and functional information, which helps segment brain tumor and gets a reliable and accurate diagnosis. Segmenting brain tumors in magnetic resonance imaging (MRI) is a challenging task because brain tumors can be at any location with changeable shape and size. Existing deep neural networks for brain tumor segmentation use few connections to fuse multilevel information. To make use of multilevel information from multimodal MRIs, we propose dual‐pathway DenseNets with fully lateral connections (DP‐DenseNets), a three‐dimensional (3D) fully convolutional neural network that uses dense connectivity to construct dual‐pathway architecture to multimodal brain tumor segmentation problem. Each two similar imaging modalities have a pathway, for one thing, the bottom‐up pathway with dense connectivity is developed for extracting features; another, the top‐down pathway concatenates the features of the bottom‐up pathway in all layers. Dual pathways with different loss functions and fully lateral connectivity from the bottom‐up pathway to the top‐down pathway provide an abundant combination of different levels of features. Comparing to these fusion schemes such as input‐level fusion and later‐level fusion, this architecture leverages semantics from low to high levels, which is provided by fully lateral connectivity. Our model is evaluated on the dataset from Brain Tumor Segmentation Challenge 2017 (BRATS 2017), and the experiments show that our method achieves better performance than other 3D networks.     

Development of automatic glioma brain tumor detection system using deep convolutional neural networks

We have developed six convolutional neural network (CNN) models for finding optimal brain tumor detection system on high-grade glioma and low-grade glioma lesions from voluminous magnetic resonance imaging human brain scans. Glioma is the most common form of brain tumor. The models are constructed based on the different combinations and settings of hyperparameters with conventional CNN architecture. The six models are two layers with five epochs, five layers with dropout, five layers with stopping criteria (FLSC), FLSC and dropout (FLSCD), FLSC and batch normalization (FLSCBN), and FLSCBN and dropout. The models were trained and tested with BraTS2013 and whole brain atlas data sets. Among them, FLSCBN model yielded the best classification results for brain tumor detection. Experimental results revealed that our deep learning approach was better than the conventional state-of-art methods.     

A comprehensive review: Segmentation of MRI images—brain tumor

Segmentation of tumors in human brain aims to classify different abnormal tissues (necrotic core, edema, active cells) from normal tissues (cerebrospinal fluid, gray matter, white matter) of the brain. In existence, detection of abnormal tissues is easy for studying brain tumor, but reproducibility, characterization of abnormalities and accuracy are complicated in the process of segmentation. The magnetic resonance imaging (MRI)‐based segmentation of tumors in brain images is more enhancing and attracting in current years of research studies. It is due to non‐invasive examination and good contrast prone to soft tissues of images obtained from MRI modality. Medical approval of different segmentation techniques depends on the benchmark and simplicity of the method. This article incorporates both fully‐automatic and semi‐automatic methods for segmentation. The outlook study of this article is to provide the summary of most significant segmentation methods of tumors in brain using MRI. © 2016 Wiley Periodicals, Inc. Int J Imaging Syst Technol, 26, 295–304, 2016     

Fully automatic method for segmentation of brain tumor from multimodal magnetic resonance images using wavelet transformation and clustering technique

Fully automatic brain tumor segmentation is one of the critical tasks in magnetic resonance imaging (MRI) images. This proposed work is aimed to develop an automatic method for brain tumor segmentation process by wavelet transformation and clustering technique. The proposed method using discrete wavelet transform (DWT) for pre‐ and post‐processing, fuzzy c‐means (FCM) for brain tissues segmentation. Initially, MRI images are preprocessed by DWT to sharpen the images and enhance the tumor region. It assists to quicken the FCM clustering technique and classified into four major classes: gray matter (GM), white matter (WM), cerebrospinal fluid (CSF), and background (BG). Then check the abnormality detection using Fuzzy symmetric measure for GM, WM, and CSF classes. Finally, DWT method is applied in segmented abnormal region of images respectively and extracts the tumor portion. The proposed method used 30 multimodal MRI training datasets from BraTS2012 database. Several quantitative measures were calculated and compared with the existing. The proposed method yielded the mean value of similarity index as 0.73 for complete tumor, 0.53 for core tumor, and 0.35 for enhancing tumor. The proposed method gives better results than the existing challenging methods over the publicly available training dataset from MICCAI multimodal brain tumor segmentation challenge and a minimum processing time for tumor segmentation. © 2016 Wiley Periodicals, Inc. Int J Imaging Syst Technol, 26, 305–314, 2016     

A rapid automatic brain tumor detection method for MRI images using modified minimum error thresholding technique

This proposed work is aimed to develop a rapid automatic method to detect the brain tumor from T2‐weighted MRI brain images using the principle of modified minimum error thresholding (MET) method. Initially, modified MET method is applied to produce well segmented and sub‐structural clarity for MRI brain images. Further, using FCM clustering the appearance of tumor area is refined. The obtained results are compared with corresponding ground truth images. The quantitative measures of results were compared with the results of those conventional methods using the metrics predictive accuracy (PA), dice coefficient (DC), and processing time. The PA and DC values of the proposed method attained maximum value and processing time is minimum while compared to conventional FCM and k‐means clustering techniques. This proposed method is more efficient and faster than the existing segmentation methods in detecting the tumor region from T2‐weighted MRI brain images. © 2015 Wiley Periodicals, Inc. Int J Imaging Syst Technol, 25, 77–85, 2015     

A fully automatic methodology for MRI brain tumour detection and segmentation

In this paper, a complete and fully automatic MRI brain tumour detection and segmentation methodology is presented as an efficient clinical-aided tool using Gaussian mixture model, Fuzzy C-Means, active contour, wavelet transform and entropy segmentation methods. The proposed algorithm is based on two main parts: the skull stripping and tumour auto-detection and segmentation. The first part was evaluated using IBSR, LPBA40 and OASIS databases, and the obtained results show that our proposed method outclasses the best popular algorithms of brain extraction with scores of 0.913, 0.954 and 0.957 for the Jaccard index, Dice coefficient and sensitivity, respectively. The second part has been evaluated using BRATS database; this methodology has achieved an accuracy of 69% of true detection, and a false detection is around 22% of healthy cases detected as tumour cases and a false detection is around 9% of tumour cases detected as healthy cases. So, the tumour segmentation performed 0.67 Jaccard index and 0.69 Dice coefficient. Our methodology is found to be a fast, effective, accurate and fully automatic one without the need to any human interaction and prior knowledge for training phases as supervised methodologies in clinical applications.     

An efficient approach for brain image (tissue) compression based on the position of the brain tumor

Medical image processing plays an important role in brain tissue detection and segmentation. In this paper, a computer aided detection of brain tissue compression based on the estimation of the location of the brain tumor. The proposed system detects and segments the brain tissues and brain tumor using mathematical morphological operations. Further, the brain tissue with tumor is compressed using lossless compression technique and the brain tissue without tumor is compressed using lossy compression technique. The proposed method achieves 96.46% sensitivity, 99.20% specificity and 98.73% accuracy for the segmentation of white matter regions from the brain. The proposed method achieves 98.16% sensitivity, 99.36% specificity and 98.78% accuracy for the segmentation of cerebrospinal fluid (CSF) regions from the brain and also achieves 93.07% sensitivity, 98.79% specificity and 97.63% accuracy for the segmentation of grey matter regions from the brain. This paper focus the brain tissue compression based on the location of brain tumor. The grey matter of the brain is applied to lossless compression due to the presence of the tumor in grey matter of the brain. The proposed system achieves 29.23% of compression ratio for compressing the grey matter of the brain region. The white matter and CSF regions of the brain are applied to lossy compression due to the non‐presence of the tumor. The proposed system achieves 39.13% of compression ratio for compressing the white matter and also achieves 37.5% of compression ratio for compressing the CSF tissue. © 2016 Wiley Periodicals, Inc. Int J Imaging Syst Technol, 26, 237–242, 2016     

3D brain magnetic resonance imaging segmentation by using bitplane and adaptive fast marching

Diagnosis using medical images helps doctors detect diseases and treat patients effectively. A system that segments objects automatically from magnetic resonance imaging (MRI) plays an important role when doctors diagnose injuries and brain diseases. This article presents a method for automatic brain, scalp, and skull segmentation from MRI that uses Bitplane and the Adaptive Fast Marching method (FMM). We focus on the segmentation of these tissues, especially the brain, because they are the essential objects, and their segmentation is the first step in the segmentation of other tissues. First, the type of each slice is set based on the shape of the brain, and the head region is segmented by removing its background. Second, the sure region and the unsure region are segmented based on the Bitplane method. Finally, this work proposes an approach for classification that is based on the Adaptive FMM. This approach is evaluated with the BrainWeb and Neurodevelopmental MRI databases and compared with other methods. The Dice Averages for brain, scalp, and skull segmentation are 96%, 80%, and 93%, respectively, on the BrainWeb database and 91%, 67%, and 80%, respectively, on the Neurodevelopmental MRI database.     

CANFIS based glioma brain tumor classification and retrieval system for tumor diagnosis

Brain tumor classification and retrieval system plays an important role in medical field. In this paper, an efficient Glioma Brain Tumor detection and its retrieval system is proposed. The proposed methodology consists of two modules as classification and retrieval. The classification modules are designed using preprocessing, feature extraction and tumor detection techniques using Co‐Active Adaptive Neuro Fuzzy Inference System (CANFIS) classifier. The image enhancement can be achieved using Heuristic histogram equalization technique as preprocessing and further texture features as Local Ternary Pattern (LTP) features and Grey Level Co‐occurrence Matrix (GLCM) features are extracted from the enhanced image. These features are used to classify the brain image into normal and abnormal using CANFIS classifier. The tumor region in abnormal brain image is segmented using normalized graph cut segmentation algorithm. The retrieval module is used to retrieve the similar segmented tumor regions from the dataset for diagnosing the tumor region using Euclidean algorithm. The proposed Glioma Brain tumor classification methodology achieves 97.28% sensitivity, 98.16% specificity and 99.14% accuracy. The proposed retrieval system achieves 97.29% precision and 98.16% recall rate with respect to ground truth images.     

Brain tumor segmentation using a deep Shuffled-YOLO network

Brain tumor is an anomalous proliferation of cells in the brain that can evolve to malignant and benign tumors. Currently, segmentation of brain tumor is the most important surgical and pharmaceutical procedures. However, manually segmenting brain tumors is hard because it is hard to find erratically shaped tumors with only one modality; the MRI modalities are integrated to provide multi-modal images with data that can be utilized to segment tumors. The recent developments in machine learning and the accessibility of medical diagnostic imaging have made it possible to tackle the challenges of segmenting brain tumors with deep neural networks. In this work, a novel Shuffled-YOLO network has been proposed for segmenting brain tumors from multimodal MRI images. Initially, the scalable range-based adaptive bilateral filer (SCRAB) pre-processing technique was used to eliminate the noise artifacts from MRI while preserving the edges. In the segmentation phase, we propose a novel deep Shuffled-YOLO architecture for segmenting the internal tumor structures that include non-enhancing, edema, necrosis, and enhancing tumors from the multi-modality MRI sequences. The experimental fallouts reveal that the proposed Shuffled-YOLO network achieves a better accuracy range of 98.07% for BraTS 2020 and 97.04% for BraTS 2019 with very minimal computational complexity compared to the state-of-the-art models.     

Fuzzy generalized fast marching method for 3D segmentation of brain structures

The aim of this work is to develop a new model for segmentation of brain structures in medical brain MR images. Brain segmentation is a challenging task due to the complex anatomical structure of brain structures as well as intensity nonuniformity, partial volume effects and noise. Generally the structures of interest are of relatively complicated size and have significant shape variations, the structures boundaries may be blurry or even missing, and the surrounding background is full of irrelevant edges. Segmentation methods based on fuzzy models have been developed to overcome the uncertainty caused by these effects. In this study, we propose a robust and accurate brain structures segmentation method based on a combination of fuzzy model and deformable model. Our method breaks up into two great parts. Initially, a preliminary stage allows to construct the various information maps, in particular a fuzzy map, used as a principal information source, constructed using the Fuzzy C‐means method (FCM). Then, a deformable model implemented with the generalized fast marching method (GFMM), evolves toward the structure to be segmented, under the action of a normal force defined from these information maps. In this sense, we used a powerful evolution function based on a fuzzy model, adapted for brain structures. Two extensions of our general method are presented in this work. The first extension concerns the addition of an edge map to the fuzzy model and the use of some rules adapted to the segmentation process. The second extension consists of the use of several models evolving simultaneously to segment several structures. Extensive experiments are conducted on both simulated and real brain MRI datasets. Our proposed approach shows promising and achieves significant improvements with respect to several state‐of‐the‐art methods and with the three practical segmentation techniques widely used in neuroimaging studies, namely SPM, FSL, and Freesurfer.