Research Article | Open Access | Download PDF
Volume 74 | Issue 2 | Year 2026 | Article Id. IJETT-V74I2P111 | DOI : https://doi.org/10.14445/22315381/IJETT-V74I2P111End-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]