Brain Tumor Segmentation with Special Emphasis on the Non-Enhancing Brain Tumor Compartment
Authors: T. Schaffer, A. Brawanski, S. Wein, A. M. Tomé, E. W. Lang
Organizations: CIML Group, Biophysics, University of Regensburg, 93040 Regensburg, Germany · Department of Neurosurgery , University Hospital Regensburg, 93042 Regensburg, Germany · Department of Biomedical Imaging, University Hospital Regensburg, 93042 Regensburg, Germany · DETI, IEETA, Universidade de Aveiro, 3810-195 Aveiro, Portugal
A U-Net based deep learning architecture is designed to segment brain tumors as they appear on various MRI modalities. Special emphasis is lent to the non-enhancing tumor compartment. The latter has not been considered anymore in recent brain tumor segmentation challenges like the MICCAI challenges. However, it is considered to be indicative of the survival time of the patient as well as of areas of further tumor growth. Hence it deems essential to have means to automatically delineate its extension within the tumor.
Figures & tables
Figure 1: Different types of residual filter blocks. Each type can be used in the above U-Net architecture
Figure 2: Two variants of the new up-scaling PAU-Net.
Figure 3: Records from the BraTS 2018 dataset [ 9 ] named CBICA-ANI-1, CBICA-AXO-1, CBICA-AQQ-1, TCIA03-419 (top to bottom). Left: Flair (CBICA-ANI-1, CBICA-AXO-1) or T1C (CBICA-AQQ-1, TCIA03-419) slice. Center: original BraTS 2018 segmentation mask (ED yellow, NCR+NET red, ET blue). Right: NCR (red) and NET (green) separated and filtered.
Model
Parameters
Input size
Training speed
Upscaling PAU-Net 5-level
13.15M
80×160×128(1.64M)
696 ms/step
Upscaling PAU-Net 4-level
2.87M
96×192×160(2.95M)
1096 ms/step
Table 1: Model comparison regarding number of parameters, input size and training speed (measured on a Tesla A100-SXM4-40GB GPU)
Figure 4: Sample record from BraTS 2021 dataset [ 8 ] . Top row from left to right: T1, T2, T1C, Flair; Bottom row left: BraTS 2021 tumor segmentation data, right: tumor segmentation data extended with NET region (yellow)
BraTS 2018 train
BraTS 2018 test
BraTS 2021 train
BraTS 2021 test
5-level
4-level
5-level
4-level
5-level
4-level
5-level
4-level
ET
0.7162
0.7179
0.7842
0.7802
0.8524
0.8566
0.8357
0.8464
TC
0.8803
0.8646
0.8125
0.8230
0.9140
0.9121
0.8798
0.8841
WT
0.9117
0.9010
0.8913
0.8912
0.9282
0.9232
0.9157
0.9186
Mean
0.8361
0.8278
0.8293
0.8315
0.8982
0.8973
0.8771
0.8830
Table 2: Upscaling PAU-Net results, Dice-Sørensen coefficients for Enhancing Tumor (ET), Tumor Core (TC) and Whole Tumor (WT)
Figure 5: Results for training the PAU-Net on BraTS 2018 subset with extracted NET segments. Training was performed with 100 epochs, 1044ms/step, learning rate 10−4 with 5% decay per epoch, training data size 68, batch size 1, GPU Tesla T4. Left: final DSCs, Right: Learning curves
Figure 6: Gamma distribution fit to volume histograms
Eval. Segment
BraTS 2018/21 Data
BraTS 2018/21 Label
Description
ET
ET
4
Enhancing Tumor
TC
ET + NCR
4,1
Tumor Core
WT
ET + NCR + NET + ED
4,1,3,2
Whole Tumor
NET
NET
3
Non-Enhancing Tumor
TCN
ET + NCR + NET
4,1,3
Tumor Core + Non-Enhancing Tumor
Table 3: Unified BraTS 2018/21 evaluation segments as compositions of data labels. NET is added as a new evaluation segment as well as TCN, which extends the traditional TC labeled segment by the NET segment.
SegResNetVAE
TSC U-Net
nnU-Net
SegResNet
nnU-Net
PAU-Net
2018 [ 67 ]
2019 [ 38 ]
2020 [ 37 ]
2021 [ 80 ]
2021 [ 56 ]
NET
0.5320
TCN
0.8846
ET
0.8145
0.8021
0.7945
0.8600
0.8823
0.8194
TC
0.8596
0.8647
0.8524
0.8868
0.9235
0.8979
WT
0.9042
0.9094
0.9119
0.9265
0.9383
0.9151
Table 4: Dice-Sørensen Coefficient test results obtained with unified 4-label BraTS 2018/21 data. Our mean values were computed from ET, TC and WT, not taking into account NET and TCN.
Accurate brain tumor segmentation from Magnetic Resonance Imaging is essential for diagnosis, treatment planning, and surgical guidance. Although Convolutional Neural Networks, particularly UNet, have achieved significant success in medical image segmentation, they often struggle to capture the long-range spatial dependencies required to model tumors with irregular shapes and complex boundaries. This paper proposes a lightweight Vision Transformer UNet that combines the hierarchical feature extraction capability of UNet with the global context modeling of Vision Transformers. The proposed architecture incorporates a compact ViT bottleneck within a U-Net encoder-decoder framework, enabling effective learning of both local and global features while maintaining computational efficiency with only 2.6 million trainable parameters. The model was evaluated on the TCGA LGG MRI Segmentation dataset, achieving a mean Intersection over Union of 0.8100 and a Dice score of 0.8446, outperforming the baseline UNet by 3.75% and 3.15%, respectively. Extensive quantitative and qualitative analyses, including confusion matrix evaluation, precision recall curves, per-image performance distribution, and tumor size dependency analysis, demonstrate the effectiveness and robustness of the proposed method for brain tumor segmentation.
Sheekar Banerjee, Md. Srabon Chowdhury, Md. Mahbub Hasan Akash +1
Brain cancer's severity necessitates precise brain tumor segmentation, which is crucial for effective brain tumor diagnosis. Manual identification, burdened by high costs, labor, and error risks, highlights the need for automated methods. In this study, we introduce the Global Context-aware Squeeze and Excite Residual UNet (GCSER-UNet), which facilitates a fusion of spatial and channel-wise attention and thus enhances the model's capacity to capture intricate spatial dependencies and contextual information. GCSER-UNet efficiently extracts tumor segments from multimodal MRI slices, delivering exceptional performance. Evaluations on benchmark databases exhibit its superiority, achieving a notable 94 percent dice score on the TCGA LGG dataset, surpassing the state-of-the-art dice score of 91.8 percent. In the BraTS 2020 dataset, the proposed GCSER-UNet ensemble approach yielded dice scores of 95 percent, 92 percent, and 90 percent for the tumor regions - Whole Tumor (W), Tumor Core (T), and Enhancing Tumor (E), respectively. The current state-of-the-art dice scores were 94 percent, 93 percent, and 88 percent. These compelling outcomes highlight the efficacy of GCSER-UNet in precise brain tumor segmentation and thus can aid neurologists in effective brain cancer management and treatment planning.
Sourjya Mukherjee, Ananya Bhattacharjee, R. Murugan
Biomedical Imaging Laboratory, Department of Electronics and Communication Engineering, National Institute of Technology Silchar, Silchar, Assam, India, 788010
Automatic brain tumor segmentation from multi-modal MRI remains challenging because volumetric models often incur substantial computational cost. This paper presents DALight-3D, a compact 3D U-Net variant that combines depthwise separable 3D convolutions, identifier-conditioned normalization, cross-slice attention, and adaptive skip fusion. The method is evaluated on the Medical Segmentation Decathlon Task01 BrainTumour benchmark under matched optimization settings against standard 3D U-Net, Attention U-Net, Residual 3D U-Net, and V-Net baselines. In the reported 50-epoch comparison, DALight-3D achieves a mean Dice of 0.727 with 2.22M parameters, compared with 0.710 Dice and 3.20M parameters for Residual 3D U-Net. Component-wise ablations show consistent performance degradation when SepConv, identifier-conditioned normalization, CSA, or SSFB is removed. These results indicate that DALight-3D offers a favorable accuracy-efficiency trade-off within the present benchmark setting.
Nand Kumar Mishra, Dhruv Mishra, Dr Manu Pratap Singh
Department of Computer Science, Dr. Bhimrao Ambedkar University, Agra, India. · Department of Computer Science and Engineering, Shiv Nadar University, Greater Noida, India.