Brain Tumour Segmentation from Multispectral MR Image Data Using Ensemble Learning Methods

A Validation Framework for Brain Tumor Segmentation

In this work, we propose a fully automatic brain tumor and edema segmentation technique in brain magnetic resonance (MR) images. Different brain tissues are characterized using the novel texture features such as piece-wise triangular prism surface area (PTPSA), multi-fractional Brownian motion (mBm) and Gabor-like textons, along with regular intensity and intensity difference features. Classical Random Forest (RF) classifier is used to formulate the segmentation task as classification of these features in multi-modal MRIs. The segmentation performance is compared with other state-of-art works using a publicly available dataset known as Brain Tumor Segmentation (BRATS) 2012 [1]. Quantitative evaluation is done using the online evaluation tool from Kitware/MIDAS website [2]. The results show that our segmentation performance is more consistent and, on the average, outperforms other state-of-the art works in both training and challenge cases in the BRATS competition.

A Review on Convolutional Neural Networks for Brain Tumor Segmentation: Methods, Datasets, Libraries, and Future Directions

Segmentation and classification of brain tumor are time-consuming and challenging chore in clinical image processing. Magnetic Resonance Imaging (MRI) offers more information related to human soft tissues that assists in diagnosing brain tumor. Precise segmentation of the MRI images is vital to diagnose brain tumor by means of computer-aided medical tools. Afterwards suitable segmentation of MRI brain tumor images, tumor classification is performed that is a hard chore owing to complications. Therefore, Gannet Aquila Optimization Algorithm_deep maxout network (GAOA_DMN) and GAOA_K-Net+speech enhancement generative adversarial network (GAOA_K-Net+Segan) is presented for classification and segmentation of brain tumor utilizing MRI images. Here, pre-processing phase performs noise removal from input image utilizing the Laplacian filter and also the region of interest (ROI) extraction is also carried out. Then, segmentation of brain tumor is conducted by K-Net+Segan, which is combined by Motyka similarity. However, K-Net+Segan for segmentation is trained by GAOA that is an amalgamation of Gannet Optimization Algorithm (GOA) and Aquila Optimizer (AO). From segmented image, features are extracted for performing classification phase. At last, brain tumor classification is conducted by DMN, which is tuned by GAOA and thus, output is obtained. Furthermore, GAOA_K-Net+Segan obtained better outcomes in terms of segmentation accuracy whereas devised GAOA_DMN achieved maximum accuracy, true negative rate (TNR) and true positive rate (TPR) of 92.7%, 94.5% and 91.5%.

Glioblastoma is an aggressive type of cancer that can develop in the brain or spinal cord. Magnetic Resonance Imaging (MRI) is key to diagnosing and tracking brain tumors in clinical settings. Brain tumor segmentation in MRI is required for disease diagnosis, surgical planning, and prognosis. As these tumors are heterogeneous in shape and appearance, their segmentation becomes a challenging task. The performance of automated medical image segmentation has considerably improved because of recent advances in deep learning. Introducing context encoding with deep CNN models has shown promise for semantic segmentation of brain tumors. In this work, we use a 3D UNet-Context Encoding (UNCE) deep learning network for improved brain tumor segmentation. Further, we introduce epistemic and aleatoric Uncertainty Quantification (UQ) using Monte Carlo Dropout (MCDO) and Test Time Augmentation (TTA) with the UNCE deep learning model to ascertain confidence in tumor segmentation performance. We build our model using the training MRI image sets of RSNA-ASNR-MICCAI Brain Tumor Segmentation (BraTS) Challenge 2021. We evaluate the model performance using the validation and test images from the BraTS challenge dataset. Online evaluation of validation data shows dice score coefficients (DSC) of 0.7787, 0.8499, and 0.9159 for enhancing tumor (ET), tumor core (TC), and whole tumor (WT), respectively. The dice score coefficients of the test datasets are 0.6684 for ET, 0.7056 for TC, and 0.7551 for WT, respectively.

Brain tumors are one of the most common neurological complications that affect millions each year. Current studies have focused only on either the segmentation of brain tumors or healthy anatomical regions. Unfortunately, there is a lack of research on whole brain segmentation of patients with existing tumors. The segmentation of these regions is cruical for understanding patient pathologies. Due to the distortions in the brain caused by tumors, whole-brain segmentation models trained on healthy brains will not perform accurately on diseased ones. To address this issue, this paper proposes a novel unified 3D nnU-Net model for the segmentation of both brain tumor and whole-brain structures for the first time. Training a model on datasets that include both healthy and cancerous brain regions could enhance the generalizability of machine learning (ML) models for performing both whole-brain segmentation and tumor segmentation tasks. Currently, there are no datasets that are publicly available for this purpose. This paper proposes to address this challenge by augmenting data from OASIS-1 and BraTS2023 to train the baseline model. The model successfully achieves a Dice Similarity Coefficient (DSC) of 0.814 for whole brain structures and 0.874 for tumor segmentation, demonstrating its effectiveness across diverse regions.

The segmentation of brain tumor plays an important role in diagnosis, treatment planning, and surgical simulation. The precise segmentation of brain tumor can help clinicians obtain its location, size, and shape information. We propose a fully automatic brain tumor segmentation method based on kernel sparse coding. It is validated with 3D multiple-modality magnetic resonance imaging (MRI). In this method, MRI images are pre-processed first to reduce the noise, and then kernel dictionary learning is used to extract the nonlinear features to construct five adaptive dictionaries for healthy tissues, necrosis, edema, non-enhancing tumor, and enhancing tumor tissues. Sparse coding is performed on the feature vectors extracted from the original MRI images, which are a patch of m×m×m around the voxel. A kernel-clustering algorithm based on dictionary learning is developed to code the voxels. In the end, morphological filtering is used to fill in the area among multiple connected components to improve the segmentation quality. To assess the segmentation performance, the segmentation results are uploaded to the online evaluation system where the evaluation metrics dice score, positive predictive value (PPV), sensitivity, and kappa are used. The results demonstrate that the proposed method has good performance on the complete tumor region (dice: 0.83; PPV: 0.84; sensitivity: 0.82), while slightly worse performance on the tumor core (dice: 0.69; PPV: 0.76; sensitivity: 0.80) and enhancing tumor (dice: 0.58; PPV: 0.60; sensitivity: 0.65). It is competitive to the other groups in the brain tumor segmentation challenge. Therefore, it is a potential method in differentiation of healthy and pathological tissues.

Image segmentation is crucial in medical science for feature extraction, analysis, and interpretation, especially brain tumor segmentation, which is challenging. Prior researchers have proposed both semi-automatic and fully automatic methods for this purpose. In the present paper, we propose a new automatic approach that combines thresholding and the Generalized Gaussian Mixture Model (GGMM) with the expectation–maximization algorithm for brain tumor segmentation from Magnetic Resonance Imaging (MRI) histogram data. Our method isolates the tumor region using a thresholding technique and then employs the GGMM to cluster the tumor’s regions. Performance analysis of our approach was performed by using ground truth pre-segmented images as a reference, and it has an excellent performance in tumor region detection with high values for metrics such as the Dice coefficient, sensitivity, accuracy, specificity, and precision. Our work was executed randomly on a dataset of nine distinct patient MRIs. The FLAIR MRI modality was used for thresholding, and the T1ce MRI modality was used for segmentation. The results seem promising, indicating successful tumor region detection and segmentation.

CLCU-Net: Cross-level connected U-shaped network with selective feature aggregation attention module for brain tumor segmentation

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.

Segmentation of brain tumors in multi-parametric magnetic resonance imaging facilitates quantitative analysis crucial for clinical trials and personalized patient care. This significantly influences clinical decision-making, encompassing diagnosis and prognosis and enhancing patient outcomes. The brain tumor segmentation (BraTS) challenge, in its 2023 edition, extended to a cluster of competitions incorporating multiple tumor types. Now, in conjunction with IEEE ISBI 2024, BraTS organizes its Generalizability Across Tumors (BraTS-GoAT) challenge. In this paper, we introduce a deep-learning-based ensemble strategy involving three state-of-the-art segmentation models. Furthermore, we also introduce a novel adaptive post-processing method, based on a cross-validated tumor-specific threshold search, designed to output enhanced accurate segmentations, ensuring generalizability across various tumor types. The evaluation of our proposed method on validation cases resulted in lesion-wise Dice scores of 0.842, 0.854, 0.872 and lesion-wise 95th-percentile Hausdorff Distance scores of 29.46, 24.67, 25.22 for the enhancing tumor, tumor core, and whole tumor, respectively.

Segmentation of a brain tumor is one of the most difficult tasks in the analysis of medical images. The purpose of brain tumor segmentation is to create an accurate outline of brain tumor areas. Gliomas are the most common type of brain tumors. Diagnosis of patients with this disease is based on the analysis of the results of magnetic resonance imaging and segmentation of the tumor boundaries manually. However, due to the time-consuming nature of the manual segmentation process and errors, there is a need for a fast and reliable automatic segmentation algorithm. In recent years, deep learning methods have shown promising effectiveness in solving various computer vision problems, such as image classification, object detection and semantic segmentation. A number of methods based on deep learning have been applied to segmentation of brain tumors, and promising results have been achieved. The article proposes a hybrid method for solving the problem of segmentation of brain tumors based on its MRI images based on the U-Net architecture, the encoder of which uses a model of a deep convolutional neural network pre-trained on a set of ImageNet images. Among such models were used VGG16, VGG19, MobileNetV2, Inception, ResNet50, EfficientNetb7, InceptionResnetV2, DenseNet201, DenseNet121. Based on the hybrid method, the TL-U-Net model was implemented, and numerical experiments were carried out to train it with different encoder models for segmentation of brain tumors based on its MRI images. Computer experiments on a set of MRI images of the brain showed the effectiveness of the proposed approach, the best encoder model turned out to be the neural network Densenet121, which provided indicators of segmentation accuracy MeanIoU=90.34%, MeanDice=94.33%, accuracy=94.17%. The obtained estimates of segmentation accuracy are comparable or exceed similar estimates obtained by other researchers.

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.

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.

Dual examiner consistency learning with dynamic receptive fields and class-balance refinement for Barely-supervised brain tumor segmentation