MORPHOLOGICAL CHARACTERIZATION OF BRAIN TUMOR TISSUE IN MRI IMAGES USING CNN AND TRANSFER LEARNING

Authors

  • Dafa Fadhilah Hilmi Universitas Negeri Malang Indonesia
  • Aji Prasetya Wibawa Universitas Negeri Malang Indonesia
  • Ardha Ardhana Putra Agustavada Universitas Negeri Malang Indonesia
  • Abdullah Sholum Universitas Negeri Malang Indonesia
  • Felix Andika Dwiyanto AGH University of Krak´ow Poland

DOI:

https://doi.org/10.26877/bioma.v15i1.3550

Keywords:

Brain Tumor, Deep Learning, Magnetic resonance imaging, Neural tissue morphology, Pattern recognition

Abstract

This study evaluates the role of computational pattern recognition as an observational method for analyzing morphological characteristics of brain tumor tissue in MRI data. A total of 6,056 labeled MRI images, including glioma, meningioma, and pituitary tumor cases, were examined. The images were standardized to maintain uniform structural representation and processed using three convolutional-based architectures: a baseline CNN, MobileNetV2, and EfficientNet-B0. Model performance was assessed using accuracy, precision, recall, F1-score, AUC-ROC, and a confusion matrix. The findings show variation in identification performance across tumor categories, with pituitary tumors consistently recognized, while misclassification predominantly occurred between glioma and meningioma. Models based on transfer learning achieved stronger agreement with the reference labels than the baseline CNN, with MobileNetV2 demonstrating the most stable performance. The recurrence of similar misclassification patterns across models suggests the presence of shared morphological characteristics in MRI representations of certain tumor types. Overall, the results support the use of computational image analysis as a structured observational framework that enables consistent evaluation of brain tumor tissue morphology in MRI, providing complementary insights for biological interpretation.

References

Abbasi, S., Lan, H., Choupan, J., Sheikh-Bahaei, N., Pandey, G., & Varghese, B. (2024). Deep learning for the harmonization of structural MRI scans: a survey. BioMedical Engineering OnLine, 23(1), 90. https://doi.org/10.1186/s12938-024-01280-6

Bahuguna, A., Ashraf, A., Kavita, Verma, S., & Negi, P. (2023). Brain Tumor Classification from MRI Scans (pp. 713–725). https://doi.org/10.1007/978-981-99-3010-4_57

Bhattacharjee, B., Debnath, B., Chandra Das, J., & De, D. (2023). Isolating Brain Tissue from Abnormal Tissue Using MRI-Based U-Net Convolutional Neural Network (pp. 721–728). https://doi.org/10.1007/978-981-99-3656-4_74

Bianchi, L., Cavarzan, F., Ciampitti, L., Cremonesi, M., Grilli, F., & Saccomandi, P. (2022). Thermophysical and mechanical properties of biological tissues as a function of temperature: a systematic literature review. International Journal of Hyperthermia, 39(1), 297–340. https://doi.org/10.1080/02656736.2022.2028908

Boaro, A., Kaczmarzyk, J. R., Kavouridis, V. K., Harary, M., Mammi, M., Dawood, H., Shea, A., Cho, E. Y., Juvekar, P., Noh, T., Rana, A., Ghosh, S., & Arnaout, O. (2022). Deep neural networks allow expert-level brain meningioma segmentation and present potential for improvement of clinical practice. Scientific Reports, 12(1), 15462. https://doi.org/10.1038/s41598-022-19356-5

Chen, Y., Lin, H., Sun, J., Pu, R., Zhou, Y., & Sun, B. (2025). Texture Feature Differentiation of Glioblastoma and Solitary Brain Metastases Based on Tumor and Tumor-brain Interface. Academic Radiology, 32(1), 400–410. https://doi.org/10.1016/j.acra.2024.08.025

Damalcheruvu, P. R., Mian, M., Sharma, S., Patro, S., Vattoth, S., Viswamitra, S., Ramakrishnaiah, R. H., Kumar, M., & Van Hemert, R. L. (2022). Meningioma or Mimic: Look Twice and Save a Life. Neurographics, 12(4), 216–232. https://doi.org/10.3174/ng.2100061

Darzi, F., & Bocklitz, T. (2024). A Review of Medical Image Registration for Different Modalities. Bioengineering, 11(8), 786. https://doi.org/10.3390/bioengineering11080786

Durga, P., & Godavarthi, D. (2024). A deep learning-based intelligent decision-making model for tumor and cancer cell identification. Bulletin of Electrical Engineering and Informatics, 13(1), 510–518. https://doi.org/10.11591/eei.v13i1.6469

Elmentaite, R., Domínguez Conde, C., Yang, L., & Teichmann, S. A. (2022). Single-cell atlases: shared and tissue-specific cell types across human organs. Nature Reviews Genetics, 23(7), 395–410. https://doi.org/10.1038/s41576-022-00449-w

Ferguson, D., Henderson, A., McInnes, E. F., Lind, R., Wildenhain, J., & Gardner, P. (2022). Infrared micro-spectroscopy coupled with multivariate and machine learning techniques for cancer classification in tissue: a comparison of classification method, performance, and pre-processing technique. The Analyst, 147(16), 3709–3722. https://doi.org/10.1039/D2AN00775D

Gu, C. (2024). Enhancing medical image classification with convolutional neural networks through transfer learning: A comprehensive review. Applied and Computational Engineering, 35(1), 280–284. https://doi.org/10.54254/2755-2721/35/20230407

Hu, B., Zhang, Z., Chen, S., Xu, Q., & Li, J. (2024). A metric for quantitative evaluation of glioma margin changes in magnetic resonance imaging. Acta Radiologica, 65(6), 645–653. https://doi.org/10.1177/02841851241229597

Imran, M. T., Shafi, I., Ahmad, J., Butt, M. F. U., Villar, S. G., Villena, E. G., Khurshaid, T., & Ashraf, I. (2024). Virtual histopathology methods in medical imaging - a systematic review. BMC Medical Imaging, 24(1), 318. https://doi.org/10.1186/s12880-024-01498-9

Ismail, A. R., Azhary, M. Z. R., & Hitam, N. A. (2025). Evaluating Adan vs. Adam: An Analysis of Optimizer Performance in Deep Learning (pp. 251–263). https://doi.org/10.1007/978-3-031-82931-4_19

Jang, H.-J., Song, I. H., & Lee, S. H. (2021). Generalizability of Deep Learning System for the Pathologic Diagnosis of Various Cancers. Applied Sciences, 11(2), 808. https://doi.org/10.3390/app11020808

Jayabharathi S, & Dr.V.Ilango. (2025). Transfer Learning Models in Medical Image Anomaly Detection. International Journal of Scientific Research in Science and Technology, 12(2), 1186–1189. https://doi.org/10.32628/IJSRST251222678

Khan, S., Azam, B., Yao, Y., & Chen, W. (2022). Deep collaborative network with alpha matte for precise knee tissue segmentation from MRI. Computer Methods and Programs in Biomedicine, 222, 106963. https://doi.org/10.1016/j.cmpb.2022.106963

Kunta, J. P. K. C., & Lepakshi, V. A. (2024). Enhancing Breast Cancer Detection Through a Tailored Convolutional Neural Network Deep Learning Approach. SN Computer Science, 5(7), 826. https://doi.org/10.1007/s42979-024-03197-2

Mathi, S., Deb, D., Chaudhuri, A. K., Joseph, L., & Biswas, S. (2025). A Review Of Convolutional Neural Networks For Medical Image Analysis: Trends And Future Directions. Journal of Neonatal Surgery, 14(7), 90–97. https://doi.org/10.63682/jns.v14i7.5117

Patrício, C., Neves, J. C., & Teixeira, L. F. (2024). Explainable Deep Learning Methods in Medical Image Classification: A Survey. ACM Computing Surveys, 56(4), 1–41. https://doi.org/10.1145/3625287

Pichaivel, M., Anbumani, G., Theivendren, P., & Gopal, M. (2022). An Overview of Brain Tumor. In Brain Tumors. IntechOpen. https://doi.org/10.5772/intechopen.100806

Piotrzkowska Wróblewska, H., Karwat, P., Żyłka, A., Dobruch Sobczak, K., Dedecjus, M., & Litniewski, J. (2025). Quantitative Ultrasound-Based Precision Diagnosis of Papillary, Follicular, and Medullary Thyroid Carcinomas Using Morphological, Structural, and Textural Features. Cancers, 17(17), 2761. https://doi.org/10.3390/cancers17172761

Rahman, M. M. (2024). Brain Cancer - MRI dataset. In Mendeley Data. Mendeley Data. https://doi.org/10.17632/mk56jw9rns.1

Resende, L. L., & Alves, C. A. P. F. (2021). Imaging of brain tumors in children: the basics—a narrative review. Translational Pediatrics, 10(4), 1138–1168. https://doi.org/10.21037/tp-20-285

Sack, I. (2022). Magnetic resonance elastography from fundamental soft-tissue mechanics to diagnostic imaging. Nature Reviews Physics, 5(1), 25–42. https://doi.org/10.1038/s42254-022-00543-2

Tampu, I. E., Eklund, A., & Haj-Hosseini, N. (2022). Inflation of test accuracy due to data leakage in deep learning-based classification of OCT images. Scientific Data, 9(1), 580. https://doi.org/10.1038/s41597-022-01618-6

Teferi, M. B., & Akinyemi, L. A. (2024). Deep Learning-Based Cross-Cancer Morphological Analysis: Identifying Histopathological Patterns in Breast and Lung Cancer. Journal of Future Artificial Intelligence and Technologies, 1(3), 235–248. https://doi.org/10.62411/faith.3048-3719-36

Ünal, H. T., & Başçiftçi, F. (2022). Evolutionary design of neural network architectures: a review of three decades of research. Artificial Intelligence Review, 55(3), 1723–1802. https://doi.org/10.1007/s10462-021-10049-5

Valverde, J. M., Imani, V., Abdollahzadeh, A., De Feo, R., Prakash, M., Ciszek, R., & Tohka, J. (2021). Transfer Learning in Magnetic Resonance Brain Imaging: A Systematic Review. Journal of Imaging, 7(4), 66. https://doi.org/10.3390/jimaging7040066

Vieira de Mello, J. P., Paixao, T. M., Berriel, R., Reyes, M., Badue, C., De Souza, A. F., & Oliveira-Santos, T. (2021). Deep Learning-based Type Identification of Volumetric MRI Sequences. 2020 25th International Conference on Pattern Recognition (ICPR), 1–8. https://doi.org/10.1109/ICPR48806.2021.9413120

Wahid, K. A., He, R., McDonald, B. A., Anderson, B. M., Salzillo, T., Mulder, S., Wang, J., Sharafi, C. S., McCoy, L. A., Naser, M. A., Ahmed, S., Sanders, K. L., Mohamed, A. S. R., Ding, Y., Wang, J., Hutcheson, K., Lai, S. Y., Fuller, C. D., & van Dijk, L. V. (2021). Intensity standardization methods in magnetic resonance imaging of head and neck cancer. Physics and Imaging in Radiation Oncology, 20, 88–93. https://doi.org/10.1016/j.phro.2021.11.001

Woo, B., & Lee, M. (2021). Comparison of tissue segmentation performance between 2D U-Net and 3D U-Net on brain MR Images. 2021 International Conference on Electronics, Information, and Communication (ICEIC), 1–4. https://doi.org/10.1109/ICEIC51217.2021.9369797

Yaqoob, A., Musheer Aziz, R., & verma, N. K. (2023). Applications and Techniques of Machine Learning in Cancer Classification: A Systematic Review. Human-Centric Intelligent Systems, 3(4), 588–615. https://doi.org/10.1007/s44230-023-00041-3

Zhao, Z., Cui, H., & Cui, H. (2025). Decoding tissue complexity: multiscale mapping of chemistry–structure–function relationships through advanced visualization technologies. Journal of Materials Chemistry B, 13(27), 7897–7918. https://doi.org/10.1039/D5TB00744E

Zhou, C., Yang, X., Wu, S., Zhong, Q., Luo, T., Li, A., Liu, G., Sun, Q., Luo, P., Deng, L., Ni, H., Tan, C., Yuan, J., Luo, Q., Hu, X., Li, X., & Gong, H. (2022). Continuous subcellular resolution three-dimensional imaging on intact macaque brain. Science Bulletin, 67(1), 85–96. https://doi.org/10.1016/j.scib.2021.08.003

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Published

2026-04-24

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How to Cite

MORPHOLOGICAL CHARACTERIZATION OF BRAIN TUMOR TISSUE IN MRI IMAGES USING CNN AND TRANSFER LEARNING. (2026). BIOMA : Jurnal Ilmiah Biologi, 15(1), 74-94. https://doi.org/10.26877/bioma.v15i1.3550