International Journal of Engineering
Trends and Technology

Research Article | Open Access | Download PDF
Volume 74 | Issue 2 | Year 2026 | Article Id. IJETT-V74I2P111 | DOI : https://doi.org/10.14445/22315381/IJETT-V74I2P111

End-to-End Brain MRI Tumor Analysis: Preprocessing, Segmentation and Classification


Priyanka Gupta, Ramandeep Sandhu

Received Revised Accepted Published
01 Nov 2025 14 Jan 2026 20 Jan 2026 14 Feb 2026

Citation :

Priyanka Gupta, Ramandeep Sandhu, "End-to-End Brain MRI Tumor Analysis: Preprocessing, Segmentation and Classification," International Journal of Engineering Trends and Technology (IJETT), vol. 74, no. 2, pp. 172-183, 2026. Crossref, https://doi.org/10.14445/22315381/IJETT-V74I2P111

Abstract

The goal of this work is to provide a simple and reproducible method that performs three tasks for brain MRI in one flow: consistent preprocessing, accurate tumor segmentation, and reliable multi-class classification. The procedure uses an open dataset organized for both tasks. Preprocessing converts every slice to a common size, applies luminance equalization to improve local contrast, binarizes masks with a fixed threshold, and normalizes images so the model receives stable inputs. A shared residual encoder feeds two light heads: a U-Net style decoder for pixel masks and a small classifier for four labels (glioma, meningioma, pituitary, no tumor). Training alternates segmentation and classification mini-batches with balanced losses, and model selection uses a composite of validation Dice and validation accuracy. The protocol reports all outputs needed for audit and reuse: learning curves, confusion matrices, segmentation overlays, and a history file with metrics. In a ten-epoch run, the method achieved Dice 0.800 and IoU about 0.667 for segmentation, and accuracy 0.929 with macro-F1 0.920 for classification on the test split. The approach is compact, easy to train on a standard workstation, and avoids heavy architecture. It is suitable as a dependable baseline for studies that need both a tumor mask and a case label, and it can be extended to new sites or tasks by adjusting the preprocessing or the loss balance without changing the core design.

Keywords

Brain MRI, Brain tumors, Classification, Deep learning, Segmentation.

References

[1] Olaf Ronneberger, Philipp Fischer, and Thomas Brox, “U-Net: Convolutional Networks for Biomedical Image Segmentation,” Medical Image Computing and Computer-Assisted Intervention-MICCAI: 18th International Conference, Munich, Germany, pp. 234-241, 2015.
[
CrossRef] [Google Scholar] [Publisher Link]

[2] Özgün Çiçek et al., “3D U-Net: Learning Dense Volumetric Segmentation from Sparse Annotations,” Medical Image Computing and Computer-Assisted Intervention-MICCAI: 19th International Conference, Athens, Greece, pp. 424-432, 2016.
[
CrossRef] [Google Scholar] [Publisher Link]

[3] Liang-Chieh Chen et al., “Encoder-Decoder with Atrous Separable Convolution for Semantic Image Segmentation,” Computer Vision-ECCV 2018: 15th European Conference, Munich, Germany, pp. 833-851, 2018.
[
CrossRef] [Google Scholar] [Publisher Link]

[4] Kaiming He et al., “Deep Residual Learning for Image Recognition,” 2016 IEEE Conference on Computer Vision and Pattern Recognition (CVPR), Las Vegas, NV, USA, pp. 770-778, 2016.
[
CrossRef] [Google Scholar] [Publisher Link]

[5] Bjoern H. Menze et al., “The Multimodal Brain Tumor Image Segmentation Benchmark (BRATS),” IEEE Transactions on Medical Imaging, vol. 34, no. 10, pp. 1993-2024, 2015.
[
CrossRef] [Google Scholar] [Publisher Link]

[6] Nicholas J. Tustison et al., “N4ITK: Improved N3 Bias Correction,” IEEE Transactions on Medical Imaging, vol. 29, no. 6, pp. 1310-1320, 2010.
[
CrossRef] [Google Scholar] [Publisher Link]

[7] Kareem A. Wahid et al., “Intensity Standardization Methods in Magnetic Resonance Imaging of Head and Neck Cancer,” Physics and Imaging in Radiation Oncology, vol. 20, pp. 88-93, 2021.
[
CrossRef] [Google Scholar] [Publisher Link]

[8] László G. Nyúl, Jayaram K. Udupa, and Xuan Zhang, “New Variants of a Method of MRI Scale Standardization,” IEEE Transactions on Medical Imaging, vol. 9, no. 2, pp. 143-150, 2000.
[
CrossRef] [Google Scholar] [Publisher Link]

[9] Khushboo Munir, Fabrizio Frezza, and Antonello Rizzi, “Deep Learning Hybrid Techniques for Brain Tumor Segmentation,” Sensors, vol. 22, no. 21, pp. 1-26, 2022.
[
CrossRef] [Google Scholar] [Publisher Link]

[10] Konstantinos Kamnitsas et al., “Efficient Multi-Scale 3D CNN with Fully Connected CRF for Accurate Brain Lesion Segmentation,” Medical Image Analysis, vol. 36, pp. 61-78, 2017.
[
CrossRef] [Google Scholar] [Publisher Link]

[11] Ozan Oktay et al., “Attention U-Net: Learning where to Look for the Pancreas,” arXiv Preprint, pp. 1-10, 2018.
[
CrossRef] [Google Scholar] [Publisher Link]

[12] Jie Hu, Li Shen, and Gang Sun, “Squeeze-and-Excitation Networks,” 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, Salt Lake City, UT, USA, pp. 7132-7141, 2018.
[
CrossRef] [Google Scholar] [Publisher Link]

[13] Zongwei Zhou et al., “UNet++: A Nested U-Net Architecture for Medical Image Segmentation,” Deep Learning in Medical Image Analysis and Multimodal Learning for Clinical Decision Support: 4th International Workshop, DLMIA 2018, and 8th International Workshop, ML-CDS 2018, Held in Conjunction with MICCAI, Granada, Spain pp. 3-11, 2018. [CrossRef] [Google Scholar] [Publisher Link]

[14] Fabian Isensee et al., “nnU-Net: A Self-Configuring Method for Deep Learning-based Biomedical Image Segmentation,” Nature Methods, vol. 18, no. 2, pp. 203-211, 2021.
[
CrossRef] [Google Scholar] [Publisher Link]

[15] Geert Litjens et al., “A Survey on Deep Learning in Medical Image Analysis,” Medical Image Analysis, vol. 42, pp. 60-88, 2017.
[
CrossRef] [Google Scholar] [Publisher Link]

[16] Aman Kamboj, Rajneesh Rani, and Jiten Chaudhary, “Deep Learning Approaches for Brain Tumor Segmentation: A Review,” 2018 First International Conference on Secure Cyber Computing and Communication (ICSCCC), Jalandhar, India, pp. 599-603, 2018.
[
CrossRef] [Google Scholar] [Publisher Link]

[17] Ramin Ranjbarzadeh et al., “Brain Tumor Segmentation based on Deep Learning and an Attention Mechanism using MRI Multi-Modalities Brain Images,” Scientific Reports, vol. 11, no. 1, pp. 1-17, 2021.
[
CrossRef] [Google Scholar] [Publisher Link]

[18] Yuanpu Xie et al., “Spatial Clockwork Recurrent Neural Network for Muscle Perimysium Segmentation,” Medical Image Computing and Computer-Assisted Intervention-MICCAI: 19th International Conference, Athens, Greece, pp. 185-193, 2016.
[
CrossRef] [Google Scholar] [Publisher Link]

[19] Jingke Yan et al., “Medical Image Segmentation Model based on Triple Gate Multilayer Perceptron,” Scientific Reports, vol. 12, no. 1, pp. 1-14, 2022.
[
CrossRef] [Google Scholar] [Publisher Link]

[20] Zan Li et al., “Residual-Attention UNet++: A Nested Residual-Attention U-Net for Medical Image Segmentation,” Applied Sciences, vol. 12, no. 14, pp. 1-19, 2022.
[
CrossRef] [Google Scholar] [Publisher Link]

[21] Guotai Wang et al., “Automatic Brain Tumor Segmentation using Convolutional Neural Networks with Test-Time Augmentation,” Brainlesion: Glioma, Multiple Sclerosis, Stroke and Traumatic Brain Injuries: 4th International Workshop, BrainLes, Held in Conjunction with MICCAI, Granada, Spain, pp. 61-72, 2019.
 [
CrossRef] [Google Scholar] [Publisher Link]

[22] M. Buda M et al., “Data from the Breast Cancer Screening-Digital Breast Tomosynthesis (bcs-dbt),” Data from The Cancer Imaging Archive, 2020.
[
Google Scholar]

[23] Hidir Selcuk Nogay, Tahir Cetin Akinci, and Musa Yilmaz, “Comparative Experimental Investigation and Application of Five Classic Pre-Trained Deep Convolutional Neural Networks Via Transfer Learning for Diagnosis of Breast Cancer,” Advances in Science and Technology. Research Journal, vol. 15, no. 3, pp. 1-8, 2021.
[
CrossRef] [Google Scholar] [Publisher Link]

[24] P. Celard et al., “A Survey on Deep Learning Applied to Medical Images: From Simple Artificial Neural Networks to Generative Models,” Neural Computing and Applications, vol. 35, no. 3, pp. 2291-2323, 2022.
[
CrossRef] [Google Scholar] [Publisher Link]

[25] Jieneng Chen et al., “TransUNet: Rethinking the U-Net Architecture Design for Medical Image Segmentation through the Lens of Transformers,” Medical Image Analysis, vol. 97, pp. 1-10, 2024.
[
CrossRef] [Google Scholar] [Publisher Link]

[26] Maruf Adewole et al., “The Brain Tumor Segmentation (BraTS) Challenge 2023: Glioma Segmentation in Sub-Saharan Africa Patient Population (BraTS-Africa),” arXiv Preprint, pp. 1-10, 2023.
[
CrossRef] [Google Scholar] [Publisher Link]

[27] Aklima Akter Lima et al., “A Comprehensive Survey on the Detection, Classification, and Challenges of Neurological Disorders,” Biology, vol. 11, no. 3, pp. 1-45, 2022.
[
CrossRef] [Google Scholar] [Publisher Link]

[28] Theresa Neubauer et al., “Soft Tissue Sarcoma Co-segmentation in Combined MRI and PET/CT Data,” Multimodal Learning for Clinical Decision Support and Clinical Image-based Procedures: 10th International Workshop, ML-CDS, and 9th International Workshop, CLIP, Held in Conjunction with MICCAI, Lima, Peru, pp. 97-105, 2020.
[
CrossRef] [Google Scholar] [Publisher Link]

[29] Zach Eaton-Rosen et al., “Towards Safe Deep Learning: Accurately Quantifying Biomarker Uncertainty in Neural Network Predictions,” Medical Image Computing and Computer Assisted Intervention-MICCAI: 21st International Conference, Granada, Spain, pp. 691-699, 2018.
[
CrossRef] [Google Scholar] [Publisher Link]

[30] Sérgio Pereira et al., “Brain Tumor Segmentation using Convolutional Neural Networks in MRI Images,” IEEE Transactions on Medical Imaging, vol. 35, no. 5, pp. 1240-1251, 2016.
[
CrossRef] [Google Scholar] [Publisher Link]

[31] Min Zhang et al., “Deep-Learning Detection of Cancer Metastases to the Brain on MRI,” Journal of Magnetic Resonance Imaging, vol. 52, no. 4, pp. 1227-1236, 2020.
[
CrossRef] [Google Scholar] [Publisher Link]

[32] S. Immaculate Joy, G. Sriram, and S. Sriram Venkatesan, “Deep CNN-based Multi-Grade Brain Tumor Classification with Enhanced Data Augmentation,” Procedia Computer Science, vol. 260, pp. 300-307, 2025.
[
CrossRef] [Google Scholar] [Publisher Link]

[33] Amin Amiri Tehrani Zade et al., “An Improved Capsule Network for Glioma Segmentation on MRI Images: A Curriculum Learning Approach,” Computers in Biology and Medicine, vol. 148, pp. 1-22, 2022.
[
CrossRef] [Google Scholar] [Publisher Link]

[34] Md. Faysal Ahamed et al., “A Review on Brain Tumor Segmentation based on Deep Learning Methods with Federated Learning Techniques,” Computerized Medical Imaging and Graphics, vol. 110, pp. 1-29, 2023.
[
CrossRef] [Google Scholar] [Publisher Link]

[35] Mohammad Hamghalam, Baiying Lei, and Tianfu Wang, “Convolutional 3D to 2D Patch Conversion for Pixel-Wise Glioma Segmentation in MRI Scans,” Brainlesion: Glioma, Multiple Sclerosis, Stroke and Traumatic Brain Injuries: 5th International Workshop, BrainLes, Held in Conjunction with MICCAI, Shenzhen, China, pp. 3-12, 2020.
[
CrossRef] [Google Scholar] [Publisher Link]

[36] Vinod Kumar Dhakshnamurthy et al., “Brain Tumor Detection and Classification using Transfer Learning Models,” Engineering Proceedings, vol. 62, no. 1, pp. 1-8, 2024.
[
CrossRef] [Google Scholar] [Publisher Link]

[37] T. Loganayagi et al., “Spinal-QDCNN: Advanced Feature Extraction for Brain Tumor Detection using MRI Images,” European Spine Journal, pp. 1-21, 2025.
[
CrossRef] [Google Scholar] [Publisher Link]

[38] Steven Amaya-Oliva, Luis Mora-Torres, and Wilfredo Ticona, “Comparison of Machine Learning and Traditional Methods for Brain Tumor Detection: A Systematic Review,” Software Engineering: Emerging Trends and Practices in System Development: Proceedings of 14th Computer Science Online Conference, Czech Republic, vol. 2, pp. 269-291, 2025. [CrossRef] [Google Scholar] [Publisher Link]

[39] Jiwen Zhou et al., “An Adaptive Multi-Stage and Adjacent-Level Feature Integration Network for Brain Tumor Image Segmentation,” Interdisciplinary Sciences: Computational Life Sciences, pp. 1-19, 2025.
 [
CrossRef] [Google Scholar] [Publisher Link]

[40] S. Priyadharshini et al., “A Successive Framework for Brain Tumor Interpretation using Yolo Variants,” Scientific Reports, vol. 15, no. 1, pp. 1-24, 2025.
[CrossRef] [Google Scholar] [Publisher Link]

[41] Anjali Jain et al., “Advanced Brain Tumor Classification from MRI Images with Vision and Swin Transformer Models,” 2025 Emerging Technologies for Intelligent Systems (ETIS), Trivandrum, India, pp. 1-5, 2025.
[
CrossRef] [Google Scholar] [Publisher Link]