Brain Tumor Segmentation Using UNet-Context Encoding Network

Magnetic resonance imaging (MRI) scans are known to suffer from a variety of acquisition artifacts as well as equipment-based variations that impact image appearance and segmentation performance. It is still unclear whether a direct relationship exists between magnetic resonance (MR) image quality metrics (IQMs) (e.g., signal-to-noise, contrast-to-noise) and segmentation accuracy. Deep learning (DL) approaches have shown significant promise for automated segmentation of brain tumors on MRI but depend on the quality of input training images. We sought to evaluate the relationship between IQMs of input training images and DL-based brain tumor segmentation accuracy toward developing more generalizable models for multi-institutional data. We trained a 3D DenseNet model on the BraTS 2020 cohorts for segmentation of tumor subregions enhancing tumor (ET), peritumoral edematous, and necrotic and non-ET on MRI; with performance quantified via a 5-fold cross-validated Dice coefficient. MRI scans were evaluated through the open-source quality control tool MRQy, to yield 13 IQMs per scan. The Pearson correlation coefficient was computed between whole tumor (WT) dice values and IQM measures in the training cohorts to identify quality measures most correlated with segmentation performance. Each selected IQM was used to group MRI scans as "better" quality (BQ) or "worse" quality (WQ), via relative thresholding. Segmentation performance was re-evaluated for the DenseNet model when (i) training on BQ MRI images with validation on WQ images, as well as (ii) training on WQ images, and validation on BQ images. Trends were further validated on independent test sets derived from the BraTS 2021 training cohorts. For this study, multimodal MRI scans from the BraTS 2020 training cohorts were used to train the segmentation model and validated on independent test sets derived from the BraTS 2021 cohort. Among the selected IQMs, models trained on BQ images based on inhomogeneity measurements (coefficient of variance, coefficient of joint variation, coefficient of variation of the foreground patch) and the models trained on WQ images based on noise measurement peak signal-to-noise ratio (SNR) yielded significantly improved tumor segmentation accuracy compared to their inverse models. Our results suggest that a significant correlation may exist between specific MR IQMs and DenseNet-based brain tumor segmentation performance. The selection of MRI scans for model training based on IQMs may yield more accurate and generalizable models in unseen validation.

Brain tumor segmentation in Magnetic Resonance Imaging (MRI) scans provides vital information to radiologists in the diagnosis and staging of disease. However, these MRI scans are often corrupted with noise during its acquisition. Traditional approaches to this problem employ denoising which leads, in general, to edge smoothing and development of artifacts in MRI slices, thereby affecting tumor segmentation performance. In this paper, we employed graph signal processing (GSP) theory to first segment tumor core in each MRI slice using graph Laplacian followed by edge-aware denoising which is performed in synergy. The paper aims to present a novel technique to tackle the two problems of segmentation and denoising both under the GSP framework. The experimental results demonstrated on simulated and clinical brain MRI datasets, show highly competitive performance both in terms of tumor core segmentation under Dice and Sensitivity measures, and in terms of edge-aware denoising under PSNR and SSIM measures.

GCAUNet: A group cross-channel attention residual UNet for slice based brain tumor segmentation

To develop a novel method based on feature selection, combining convolutional neural network (CNN) and ensemble learning (EL), to achieve high accuracy and efficiency of glioma detection and segmentation using multiparametric MRIs. We proposed an evolutionary feature selection-based hybrid approach for glioma detection and segmentation on 4MR sequences (T2-FLAIR, T1, T1Gd, and T2). First, we trained a lightweight CNN to detect glioma and mask the suspected region to process large batch of MRI images. Second, we employed a differential evolution algorithm to search a feature space, which composed of 416-dimensions radiomics features extracted from four sequences of MRIs and 128-dimensions high-order features extracted by the CNN, to generate an optimal feature combination for pixel classification. Finally, we trained an EL classifier using the optimal feature combination to segment whole tumor (WT) and its subregions including non-enhancing tumor (NET), peritumoral edema (ED), and enhancing tumor (ET) in the suspected region. Experiments were carried out on 300 glioma patients from the BraTS2019 dataset using fivefold cross-validation, and the model was independently validated using the rest 35 patients from the same database. The approach achieved a detection accuracy of 98.8% using four MRIs. The Dice coefficients (and standard deviations) were 0.852±0.057, 0.844±0.046, and 0.799±0.053 for segmentation of WT (NET+ET+ED), tumor core (NET+ET), and ET, respectively. The sensitivities and specificities were 0.873±0.074, 0.863±0.072, and 0.852±0.082; the specificities were 0.994±0.005, 0.994±0.005, and 0.995±0.004 for the WT, tumor core, and ET, respectively. The performances and calculation times were compared with the state-of-the-art approaches, our approach yielded a better overall performance with average processing time of 139.5s per set of four sequence MRIs. We demonstrated a robust and computational cost-effective hybrid segmentation approach for glioma and its subregions on multi-sequence MR images. The proposed approach can be used for automated target delineation for glioma patients.

We developed a fully automated method for brain tumor segmentation using deep learning; 285 brain tumor cases with multiparametric magnetic resonance images from the BraTS2018 data set were used. We designed 3 separate 3D-Dense-UNets to simplify the complex multiclass segmentation problem into individual binary-segmentation problems for each subcomponent. We implemented a 3-fold cross-validation to generalize the network's performance. The mean cross-validation Dice-scores for whole tumor (WT), tumor core (TC), and enhancing tumor (ET) segmentations were 0.92, 0.84, and 0.80, respectively. We then retrained the individual binary-segmentation networks using 265 of the 285 cases, with 20 cases held-out for testing. We also tested the network on 46 cases from the BraTS2017 validation data set, 66 cases from the BraTS2018 validation data set, and 52 cases from an independent clinical data set. The average Dice-scores for WT, TC, and ET were 0.90, 0.84, and 0.80, respectively, on the 20 held-out testing cases. The average Dice-scores for WT, TC, and ET on the BraTS2017 validation data set, the BraTS2018 validation data set, and the clinical data set were as follows: 0.90, 0.80, and 0.78; 0.90, 0.82, and 0.80; and 0.85, 0.80, and 0.77, respectively. A fully automated deep learning method was developed to segment brain tumors into their subcomponents, which achieved high prediction accuracy on the BraTS data set and on the independent clinical data set. This method is promising for implementation into a clinical workflow.

Accurate detection and pixel‐wise classification of brain tumors in Magnetic Resonance Imaging (MRI) scans are vital for their diagnosis, prognosis study and treatment planning. Manual segmentation of tumors from MRI is highly subjective and tedious. With recent advances in deep learning, automatic brain tumor segmentation is an emerging research direction in the medical imaging domain. We present a study to improve the automatic segmentation process by introducing size variability in the Convolutional Neural Network (CNN). For pixel‐wise classification of tumorous slices convolutional neural network‐based encoder‐decoder UNET model is referred. A multi‐inception‐UNET model is proposed to improve scalability of the UNET model. Extensive experiments have been performed using the Brain Tumor Segmentation Challenge (BRATS) datasets to establish the validity of our proposed model. Experimental results show that our proposed method achieved the best results on BraTS 2015, 2017 and 2019 datasets for complete tumor, core tumor and enhancing tumor regions respectively.

In this paper, we propose an automated approach based on the geometric median shift algorithm over Riemannian manifolds, for the brain tumor detection and segmentation in magnetic resonance images (MRI). This approach is based on the geometric median, geodesic distance. We propose the median shift to overcome the limitation of mean which is not necessary a point in a set. The geodesic distance can describe data points distributed on a manifold, compared to the Euclidean distance, and produce efficient results for image analysis. Coupled with k-means algorithm, the proposed framework can cluster the brain image into tree regions (gray matter, white matter and cerebrospinal fluid) and abnormalities regions. We applied this approach to clustering the brain tissues and brain tumor segmentation, which is validated on a synthetic brain MRI. The obtained results using two datasets show the efficiency of the used algorithm validated qualitatively by the measurement of Dice Similarity Coefficient.

The brain is considered a main important part of human body as it participate to control all the activities of human. Under some unhealthy conditions the abnormal and uncontrolled growth of tissue may take place which is unnatural process. This kind of process taking place in human brain is referred as “brain tumor”. The brain tumor may be of cancerous (malignant) or may be of non-cancerous (Benign) and its detection is a very much important to reduced the death rate of humans suffering from tumor. The detection of brain tumor can be performed by using various image processing techniques like brain magnetic resonance imaging (MRI), Computed Tomography (CT), Electroencephalography (EEG), Positron Emission Tomography (PET), Magneto Encephalography (MEG) etc. Among these techniques the brain MRI is widely adopted in the world due to its significant features. But to detect tumor in the brain MRI, the processes like preprocessing, segmentation and classification are must. This paper deals with the various aspects of the brain tumor detection. The paper discusses the significant researches which are meant for brain tumor detection through MRI quality enhancement, MRI segmentation and MRI classification (as cancerous or not). The outcome of the paper discussed that there were no proper researches are performed to detect the brain tumor, focused on good quality of image, less researches on segmentation and classification of brain tumor. Finally the paper gives the future research scope to overcome the addressed research gap.

Brain tumor segmentation in magnetic resonance imaging (MRI) is considered a complex procedure because of the variability of tumor shapes and the complexity of determining the tumor location, size, and texture. Manual tumor segmentation is a time-consuming task highly prone to human error. Hence, this study proposes an automated method that can identify tumor slices and segment the tumor across all image slices in volumetric MRI brain scans. First, a set of algorithms in the pre-processing stage is used to clean and standardize the collected data. A modified gray-level co-occurrence matrix and Analysis of Variance (ANOVA) are employed for feature extraction and feature selection, respectively. A multi-layer perceptron neural network is adopted as a classifier, and a bounding 3D-box-based genetic algorithm is used to identify the location of pathological tissues in the MRI slices. Finally, the 3D active contour without edge is applied to segment the brain tumors in volumetric MRI scans. The experimental dataset consists of 165 patient images collected from the MRI Unit of Al-Kadhimiya Teaching Hospital in Iraq. Results of the tumor segmentation achieved an accuracy of 89% ± 4.7% compared with manual processes.

Today also, radiologist analyze the MR images manually based on their experience and knowledge for segmenting the tumor. Use some graphical software to make the report about the presence of the tumor, its size, and other features. Based on this report doctors diagnose the patient, it is the main source for any doctor to start the treatment of the patient. However, as the MRI reports are based on the experience of the radiologist so it is a big challenge to maintain uniformity in the reports generated from the different MR imaging centers. Therefore, automation in this particular field is very much required for better precision and to maintain uniformity in the report. Therefore, doctor can diagnose the patient in much better way. Deep learning playing a vital role in automating the process of brain tumor and other organ segmentation using MR images. Many researchers developed various state-of-art methods to automate the process of brain tumor segmentation in MR images. There are multiple deep learning methods such as stacked auto- encoder, artificial neural network, convolutional neural network, and Unet used for the process of segmenting the medial images, where CNN is the most successful method for segmenting. In this chapter, the importance of automatic brain tumor segmentation approach. CNN and process of convolution, max pooling discussed in detail. Moreover, application of CNN for automatically segmenting brain tumor also discussed with some state-of-art methods.

A Validation Framework for Brain Tumor Segmentation

Contrastive learning, a successful form of representational learning, has shown promising results in pretraining deep learning (DL) models for downstream tasks. When working with limited annotation data, as in medical image segmentation tasks, learning domain-specific local representations can further improve the performance of DL models. In this work, we extend the contrastive learning framework to utilize domain-specific contrast information from unlabeled Magnetic Resonance (MR) images to improve the performance of downstream MR image segmentation tasks in the presence of limited labeled data. The contrast in MR images is controlled by underlying tissue properties (e.g., T1 or T2) and image acquisition parameters. We hypothesize that learning to discriminate local representations based on underlying tissue properties should improve subsequent segmentation tasks on MR images. We propose a novel constrained contrastive learning (CCL) strategy that uses tissue-specific information via a constraint map to define positive and negative local neighborhoods for contrastive learning, embedding this information in the representational space during pretraining. For a given MR contrast image, the proposed strategy uses local signal characteristics (constraint map) across a set of related multi-contrast MR images as a surrogate for underlying tissue information. We demonstrate the utility of the approach for downstream: (1) multi-organ segmentation tasks in T2-weighted images where a DL model learns T2 information with constraint maps from a set of 2D multi-echo T2-weighted images (n=101) and (2) tumor segmentation tasks in multi-parametric images from the public brain tumor segmentation (BraTS) (n=80) dataset where DL models learn T1 and T2 information from multi-parametric BraTS images. Performance is evaluated on downstream multi-label segmentation tasks with limited data in (1) T2-weighted images of the abdomen from an in-house Radial-T2 (Train/Test=30/20), (2) public Cartesian-T2 (Train/Test=6/12) dataset, and (3) multi-parametric MR images from the public brain tumor segmentation dataset (BraTS) (Train/Test=40/50). The performance of the proposed CCL strategy is compared to state-of-the-art self-supervised contrastive learning techniques. In each task, a model is also trained using all available labeled data for supervised baseline performance. The proposed CCL strategy consistently yielded improved Dice scores, Precision, and Recall metrics, and reduced HD95 values across all segmentation tasks. We also observed performance comparable to the baseline with reduced annotation effort. The t-SNE visualization of features for T2-weighted images demonstrates its ability to embed T2 information in the representational space. On the BraTS dataset, we also observed that using an appropriate multi-contrast space to learn T1+T2, T1, or T2 information during pretraining further improved the performance of tumor segmentation tasks. Learning to embed tissue-specific information that controls MR image contrast with the proposed constrained contrastive learning improved the performance of DL models on subsequent segmentation tasks compared to conventional self-supervised contrastive learning techniques. The use of such domain-specific local representations could help understand, improve performance, and mitigate the scarcity of labeled data in MR image segmentation tasks.

In this paper, we look at how to design and build a system to find tumors using 2 Convolutional Neural Network (CNN) models. With the help of digital image processing and deep Learning, we can make a system that automatically diagnoses and finds different diseases and abnormalities. The tumor detection system may include image enhancement, segmentation, data enhancement, feature extraction, and classification. These options are set up so that the CNN model can give the best results. During the training phase, the learning rate is used to change the weights and bias. The learning rate also changes the weights. One Epoch is when all of the training images are shown to the model. As the training data may be very large, the data in each epoch are split into batches. Every epoch has a training session and a test session. After each epoch, the weights are changed based on how fast the CNN is learning. This is done with the help of optimization algorithms. The suggested technique uses the anticipated mean intersection over union value to identify failure instances in addition to forecasting the mean intersection over union. This paper talks about how to separate brain tumors from magnetic resonance images of patients taken from "Brain web." Using basic ideas of digital image processing, magnetic resonance images are used to extract and find tumors using a hybrid method. In this paper, the proposed algorithm is applied with the help of MATLAB. In medical image processing, brain tumor segmentation is an important task. The goal of this paper is to look at different ways to divide brain tumors using magnetic resonance imaging. Recently, automatic segmentation using deep learning methods has become popular because these methods get the best results and are better at solving this problem than others. Deep learning methods can also be used to process and evaluate large amounts of magnetic resonance imaging image data quickly and objectively. A classification method based on a convolution neural network is also added to the proposed scheme to make it more accurate and cut down on the amount of time it takes to do the calculations. Also, the results of the classification are given as images of a tumor or a healthy brain. The training is 98.5% correct. In the same way, both the validation accuracy and validation loss are high.

Intracranial tumors are commonly known as brain tumors, which can be life-threatening in severe cases. Magnetic resonance imaging (MRI) is widely used in diagnosing brain tumors because of its harmless to the human body and high image resolution. Due to the heterogeneity of brain tumor height, MRI imaging is exceptionally irregular. How to accurately and quickly segment brain tumor MRI images is still one of the hottest topics in the medical image analysis community. However, according to the brain tumor segmentation algorithms, we could find now, most segmentation algorithms still stay in two-dimensional (2D) image segmentation, which could not obtain the spatial dependence between features effectively. In this study, we propose a brain tumor automatic segmentation method called scSE-NL V-Net. We try to use three-dimensional (3D) data as the model input and process the data by 3D convolution to get some relevance between dimensions. Meanwhile, we adopt non-local block as the self-attention block, which can reduce inherent image noise interference and make up for the lack of spatial dependence due to convolution. To improve the accuracy of convolutional neural network (CNN) image recognition, we add the “Spatial and Channel Squeeze-and-Excitation” Network (scSE-Net) to V-Net. The dataset used in this paper is from the brain tumor segmentation challenge 2020 database. In the test of the official BraTS2020 verification set, the Dice similarity coefficient is 0.65, 0.82, and 0.76 for the enhanced tumor (ET), whole tumor (WT), and tumor core (TC), respectively. Thereby, our model can make an auxiliary effect on the diagnosis of brain tumors established.

The number of medical imaging devices is quickly and steadily rising, generating an increasing amount of image records day by day. The number of qualified human experts able to handle this data cannot follow this trend, so there is a strong need to develop reliable automatic segmentation and decision support algorithms. The Brain Tumor Segmentation Challenge (BraTS), first organized seven years ago, provoked a strong intensification of the development of brain tumor detection and segmentation algorithms. Beside many others, several ensemble learning solutions have been proposed lately to the above mentioned problem. This study presents an evaluation framework developed to evaluate the accuracy and efficiency of these algorithms deployed in brain tumor segmentation, based on the BraTS 2016 train data set. All evaluated algorithms proved suitable to provide acceptable accuracy in segmentation, but random forest was found the best, both in terms of precision and efficiency.