brain tumor segmentation
Novel Deep Learning Architectures for Classification and Segmentation of Brain Tumors from MRI Images
Brain tumors pose a significant threat to human life, therefore it is very much necessary to detect them accurately in the early stages for better diagnosis and treatment. Brain tumors can be detected by the radiologist manually from the MRI scan images of the patients. However, the incidence of brain tumors has risen amongst children and adolescents in recent years, resulting in a substantial volume of data, as a result, it is time-consuming and difficult to detect manually. With the emergence of Artificial intelligence in the modern world and its vast application in the medical field, we can make an approach to the CAD (Computer Aided Diagnosis) system for the early detection of Brain tumors automatically. All the existing models for this task are not completely generalized and perform poorly on the validation data. So, we have proposed two novel Deep Learning Architectures - (a) SAETCN (Self-Attention Enhancement Tumor Classification Network) for the classification of different kinds of brain tumors. We have achieved an accuracy of 99.38% on the validation dataset making it one of the few Novel Deep learning-based architecture that is capable of detecting brain tumors accurately. We have trained the model on the dataset, which contains images of 3 types of tumors (glioma, meningioma, and pituitary tumors) and non-tumor cases. We have achieved an overall pixel accuracy of 99.23%. Introduction Brain Tumors are a huge concern in the field of medicine because of their high mortality rate. Brain tumor forms when there is an uncontrollable abnormal growth of the cells within the Brain. The abnormal growth may occur in the brain itself which is called a primary tumor or it may spread to the brain from the other parts of the body which are called secondary or metastatic tumors [8]. The proper reason and causes of brain tumors are not yet understood but according to researchers, they occur due to genetic mutations that affect cell growth and division [6]. This mutation can cause the cell to multiply causing the tumor.
The MICCAI Federated Tumor Segmentation (FeTS) Challenge 2024: Efficient and Robust Aggregation Methods for Federated Learning
Linardos, Akis, Pati, Sarthak, Baid, Ujjwal, Edwards, Brandon, Foley, Patrick, Ta, Kevin, Chung, Verena, Sheller, Micah, Khan, Muhammad Irfan, Jafaritadi, Mojtaba, Kontio, Elina, Khan, Suleiman, Mรคchler, Leon, Ezhov, Ivan, Shit, Suprosanna, Paetzold, Johannes C., Grimberg, Gustav, Nickel, Manuel A., Naccache, David, Siomos, Vasilis, Passerat-Palmbach, Jonathan, Tarroni, Giacomo, Kim, Daewoon, Klausmann, Leonard L., Shah, Prashant, Menze, Bjoern, Makris, Dimitrios, Bakas, Spyridon
We present the design and results of the MICCAI Federated Tumor Segmentation (FeTS) Challenge 2024, which focuses on federated learning (FL) for glioma sub-region segmentation in multi-parametric MRI and evaluates new weight aggregation methods aimed at improving robustness and efficiency. Six participating teams were evaluated using a standardized FL setup and a multi-institutional dataset derived from the BraTS glioma benchmark, consisting of 1,251 training cases, 219 validation cases, and 570 hidden test cases with segmentations for enhancing tumor (ET), tumor core (TC), and whole tumor (WT). Teams were ranked using a cumulative scoring system that considered both segmentation performance, measured by Dice Similarity Coefficient (DSC) and the 95th percentile Hausdorff Distance (HD95), and communication efficiency assessed through the convergence score. A PID-controller-based method achieved the top overall ranking, obtaining mean DSC values of 0.733, 0.761, and 0.751 for ET, TC, and WT, respectively, with corresponding HD95 values of 33.922 mm, 33.623 mm, and 32.309 mm, while also demonstrating the highest communication efficiency with a convergence score of 0.764. These findings advance the state of federated learning for medical imaging, surpassing top-performing methods from previous challenge iterations and highlighting PID controllers as effective mechanisms for stabilizing and optimizing weight aggregation in FL. The challenge code is available at https://github.com/FeTS-AI/Challenge.
CCSD: Cross-Modal Compositional Self-Distillation for Robust Brain Tumor Segmentation with Missing Modalities
Xie, Dongqing, Wu, Yonghuang, Ai, Zisheng, Min, Jun, Jiang, Zhencun, Geng, Shaojin, Wang, Lei
The accurate segmentation of brain tumors from multi-modal MRI is critical for clinical diagnosis and treatment planning. While integrating complementary information from various MRI sequences is a common practice, the frequent absence of one or more modalities in real-world clinical settings poses a significant challenge, severely compromising the performance and generalizability of deep learning-based segmentation models. To address this challenge, we propose a novel Cross-Modal Compositional Self-Distillation (CCSD) framework that can flexibly handle arbitrary combinations of input modalities. CCSD adopts a shared-specific encoder-decoder architecture and incorporates two self-distillation strategies: (i) a hierarchical modality self-distillation mechanism that transfers knowledge across modality hierarchies to reduce semantic discrepancies, and (ii) a progressive modality combination distillation approach that enhances robustness to missing modalities by simulating gradual modality dropout during training. Extensive experiments on public brain tumor segmentation benchmarks demonstrate that CCSD achieves state-of-the-art performance across various missing-modality scenarios, with strong generalization and stability.
Knowledge-Guided Brain Tumor Segmentation via Synchronized Visual-Semantic-Topological Prior Fusion
Background: Brain tumor segmentation requires precise delineation of hierarchical structures from multi-sequence MRI. However, existing deep learning methods primarily rely on visual features, showing insufficient discriminative power in ambiguous boundary regions. Moreover, they lack explicit integration of medical domain knowledge such as anatomical semantics and geometric topology. Methods: We propose a knowledge-guided framework, Synchronized Tri-modal Prior Fusion (STPF), that explicitly integrates three heterogeneous knowledge priors: pathology-driven differential features (T1ce-T1, T2-FLAIR, T1/T2) encoding contrast patterns; unsupervised semantic descriptions transformed into voxel-level guidance via spatialization operators; and geometric constraints extracted through persistent homology analysis. A dual-level fusion architecture dynamically allocates prior weights at the voxel level based on confidence and at the sample level through hypernetwork-generated conditional vectors. Furthermore, nested output heads structurally ensure the hierarchical constraint ET subset TC subset WT. Results: STPF achieves a mean Dice coefficient of 0.868 on the BraTS 2020 dataset, surpassing the best baseline by 2.6 percentage points (3.09% relative improvement). Notably, five-fold cross-validation yields coefficients of variation between 0.23% and 0.33%, demonstrating stable performance. Additionally, ablation experiments show that removing topological and semantic priors leads to performance degradation of 2.8% and 3.5%, respectively. Conclusions: By explicitly integrating medical knowledge priors - anatomical semantics and geometric constraints - STPF improves segmentation accuracy in ambiguous boundary regions while demonstrating generalization capability and clinical deployment potential.
Efficient Meningioma Tumor Segmentation Using Ensemble Learning
Pajouh, Mohammad Mahdi Danesh, Saeedi, Sara
Meningiomas represent the most prevalent form of primary brain tumors, comprising nearly one-third of all diagnosed cases. Accurate delineation of these tumors from MRI scans is crucial for guiding treatment strategies, yet remains a challenging and time-consuming task in clinical practice. Recent developments in deep learning have accelerated progress in automated tumor segmentation; however, many advanced techniques are hindered by heavy computational demands and long training schedules, making them less accessible for researchers and clinicians working with limited hardware. In this work, we propose a novel ensemble-based segmentation approach that combines three distinct architectures: (1) a baseline SegResNet model, (2) an attention-augmented SegResNet with concatenative skip connections, and (3) a dual-decoder U-Net enhanced with attention-gated skip connections (DDUNet). The ensemble aims to leverage architectural diversity to improve robustness and accuracy while significantly reducing training demands. Each baseline model was trained for only 20 epochs and Evaluated on the BraTS-MEN 2025 dataset. The proposed ensemble model achieved competitive performance, with average Lesion-Wise Dice scores of 77.30%, 76.37% and 73.9% on test dataset for Enhancing Tumor (ET), Tumor Core (TC) and Whole Tumor (WT) respectively. These results highlight the effectiveness of ensemble learning for brain tumor segmentation, even under limited hardware constraints. Our proposed method provides a practical and accessible tool for aiding the diagnosis of meningioma, with potential impact in both clinical and research settings.
Multimodal Fusion at Three Tiers: Physics-Driven Data Generation and Vision-Language Guidance for Brain Tumor Segmentation
Accurate brain tumor segmentation is crucial for neuro-oncology diagnosis and treatment planning. Deep learning methods have made significant progress, but automatic segmentation still faces challenges. These include tumor morphological heterogeneity and complex three-dimensional spatial relationships. This paper proposes a three-tier fusion architecture that achieves precise brain tumor segmentation. The method processes information progressively at the pixel, feature, and semantic levels. At the pixel level, physical modeling extends magnetic resonance imaging (MRI) to multimodal data. This includes simulated ultrasound and synthetic computed tomography (CT). At the feature level, the method achieves Transformer-based cross-modal feature fusion through multi-teacher collaborative distillation. At the semantic level, clinical textual knowledge generated by GPT-4V transforms into spatial guidance signals. This transformation uses Contrastive Language-Image Pre-training (CLIP) contrastive learning and Feature-wise Linear Modulation (FiLM). These three tiers work together to form a complete processing chain. The chain spans from data augmentation to feature extraction to semantic guidance. The model achieves average Dice coefficients of 0.8665, 0.9014, and 0.8912 on the three datasets, respectively. The 95% Hausdorff Distance (HD95) reduces by an average of 6.57 millimeters compared to the baseline. Introduction Magnetic resonance imaging (MRI) segmentation of brain tumors is fundamental for neuro-oncology diagnosis and treatment planning. Different sub-regions have different prognostic significance.
Post-Processing Methods for Improving Accuracy in MRI Inpainting
Kulkarni, Nishad, Iyer, Krithika, Tapp, Austin, Parida, Abhijeet, Capellรกn-Martรญn, Daniel, Jiang, Zhifan, Ledesma-Carbayo, Marรญa J., Anwar, Syed Muhammad, Linguraru, Marius George
Magnetic Resonance Imaging (MRI) is the primary imaging modality used in the diagnosis, assessment, and treatment planning for brain pathologies. However, most automated MRI analysis tools, such as segmentation and registration pipelines, are optimized for healthy anatomies and often fail when confronted with large lesions such as tumors. To overcome this, image inpainting techniques aim to locally synthesize healthy brain tissues in tumor regions, enabling the reliable application of general-purpose tools. In this work, we systematically evaluate state-of-the-art inpainting models and observe a saturation in their standalone performance. In response, we introduce a methodology combining model ensembling with efficient post-processing strategies such as median filtering, histogram matching, and pixel averaging. Further anatomical refinement is achieved via a lightweight U-Net enhancement stage. Comprehensive evaluation demonstrates that our proposed pipeline improves the anatomical plausibility and visual fidelity of inpainted regions, yielding higher accuracy and more robust outcomes than individual baseline models. By combining established models with targeted post-processing, we achieve improved and more accessible in-painting outcomes, supporting broader clinical deployment and sustainable, resource-conscious research.
Towards Label-Free Brain Tumor Segmentation: Unsupervised Learning with Multimodal MRI
Comas-Quiles, Gerard, Garcia-Cabrera, Carles, Dietlmeier, Julia, O'Connor, Noel E., Marques, Ferran
Unsupervised anomaly detection (UAD) presents a complementary alternative to supervised learning for brain tumor segmentation in magnetic resonance imaging (MRI), particularly when annotated datasets are limited, costly, or inconsistent. In this work, we propose a novel Multimodal Vision Transformer Autoencoder (MViT-AE) trained exclusively on healthy brain MRIs to detect and localize tumors via reconstruction-based error maps. This unsupervised paradigm enables segmentation without reliance on manual labels, addressing a key scalability bottleneck in neuroimaging workflows. Our method is evaluated in the BraTS-GoAT 2025 Lighthouse dataset, which includes various types of tumors such as gliomas, meningiomas, and pediatric brain tumors. To enhance performance, we introduce a multimodal early-late fusion strategy that leverages complementary information across multiple MRI sequences, and a post-processing pipeline that integrates the Segment Anything Model (SAM) to refine predicted tumor contours. Despite the known challenges of UAD, particularly in detecting small or non-enhancing lesions, our method achieves clinically meaningful tumor localization, with lesion-wise Dice Similarity Coefficient of 0.437 (Whole Tumor), 0.316 (Tumor Core), and 0.350 (Enhancing Tumor) on the test set, and an anomaly Detection Rate of 89.4% on the validation set. These findings highlight the potential of transformer-based unsupervised models to serve as scalable, label-efficient tools for neuro-oncological imaging.
An Empirical Study on MC Dropout--Based Uncertainty--Error Correlation in 2D Brain Tumor Segmentation
Accurate brain tumor segmentation from MRI is vital for diagnosis and treatment planning. Although Monte Carlo (MC) Dropout is widely used to estimate model uncertainty, its effectiveness in identifying segmentation errors -- especially near tumor boundaries -- remains unclear. This study empirically examines the relationship between MC Dropout--based uncertainty and segmentation error in 2D brain tumor MRI segmentation using a U-Net trained under four augmentation settings: none, horizontal flip, rotation, and scaling. Uncertainty was computed from 50 stochastic forward passes and correlated with pixel-wise errors using Pearson and Spearman coefficients. Results show weak global correlations ($r \approx 0.30$--$0.38$) and negligible boundary correlations ($|r| < 0.05$). Although differences across augmentations were statistically significant ($p < 0.001$), they lacked practical relevance. These findings suggest that MC Dropout uncertainty provides limited cues for boundary error localization, underscoring the need for alternative or hybrid uncertainty estimation methods in medical image segmentation.
Reproducible Evaluation of Data Augmentation and Loss Functions for Brain Tumor Segmentation
Brain tumor segmentation is crucial for diagnosis and treatment planning, yet challenges such as class imbalance and limited model generalization continue to hinder progress. This work presents a reproducible evaluation of U-Net segmentation performance on brain tumor MRI using focal loss and basic data augmentation strategies. Experiments were conducted on a publicly available MRI dataset, focusing on focal loss parameter tuning and assessing the impact of three data augmentation techniques: horizontal flip, rotation, and scaling. The U-Net with focal loss achieved a precision of 90%, comparable to state-of-the-art results. By making all code and results publicly available, this study establishes a transparent, reproducible baseline to guide future research on augmentation strategies and loss function design in brain tumor segmentation.