Skip to main content
Log in

Improved U-Net architecture with VGG-16 for brain tumor segmentation

  • Scientific Paper
  • Published:
Physical and Engineering Sciences in Medicine Aims and scope Submit manuscript

Abstract

Automated assessment and segmentation of Brain MRI images facilitate towards detection of neurological diseases and disorders. In this paper, we propose an improved U-Net with VGG-16 to segment Brain MRI images and identify region-of-interest (tumor cells). We compare results of improved U-Net with a custom-designed U-Net architecture by analyzing the TCGA-LGG dataset (3929 images) from the TCI archive, and achieve pixel accuracies of 0.994 and 0.9975 from basic U-Net and improved U-Net architectures, respectively. Our results outperformed common CNN-based state-of-the-art works.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

References

  1. Ronneberger O, Fischer P, Brox T (2015) U-net: convolutional networks for biomedical image segmentation. International conference on medical image computing and computer-assisted intervention. Springer, Cham, pp 234–241

    Google Scholar 

  2. Lin T-Y, Dollár P, Girshick R, He K, Hariharan B, Belongie S (2017) Feature pyramid networks for object detection. In: Proceedings of the IEEE conference on computer vision and pattern recognition, pp 2117–2125

  3. Christ PF, Elshaer MEA, Ettlinger F, Tatavarty S, Bickel M, Bilic P, Rempfler M, Armbruster M, Hofmann F, D’Anastasi M, et al (2016) Automatic liver and lesion segmentation in CT using cascaded fully convolutional neural networks and 3D conditional random fields. In: International conference on medical image computing and computer-assisted intervention. Springer, pp 415–423

  4. Menze BH, Jakab A, Bauer S, Kalpathy-Cramer Farahani K, Kirby J, Burren Y, Porz N, Slotboom J, Wiest R et al (2014) The multimodal brain tumor image segmentation benchmark (BRATS). IEEE Trans Med Imaging 34(10):1993–2024

    Article  Google Scholar 

  5. Bengio Y, Courville A, Vincent P (2013) Representation learning: a review and new perspectives. IEEE Trans Pattern Anal Mach Intell 35(8):1798–1828

    Article  Google Scholar 

  6. Havaei M, Davy A, Warde-Farley D, Biard A, Courville A, Bengio Y, Pal C, Jodoin P-M, Larochelle H (2017) Brain tumor segmentation with deep neural networks. Med Image Anal 35:18–31

    Article  Google Scholar 

  7. Pereira S, Pinto A, Alves V, Silva CA (2016) Brain tumor segmentation using convolutional neural networks in MRI images. IEEE Trans Med Imaging 35(5):1240–1251

    Article  Google Scholar 

  8. Kamnitsas K, Ledig C, Newcombe VFJ, Simpson JP, Kane AD, Menon DK, Rueckert D, Glocker B (2017) Efficient multi-scale 3D CNN with fully connected CRF for accurate brain lesion segmentation. Med Image Anal 36:61–78

    Article  Google Scholar 

  9. Dvořák P, Menze B (2015) Local structure prediction with convolutional neural networks for multimodal brain tumor segmentation. In: International MICCAI workshop on medical computer vision. Springer, pp 59–71

  10. Brosch T, Tang LYW, Yoo Y, Li DKB, Traboulsee A, Tam R (2016) Deep 3D convolutional encoder networks with shortcuts for multiscale feature integration applied to multiple sclerosis lesion segmentation. IEEE Trans Med Imaging 35(5):1229–1239

    Article  Google Scholar 

  11. Dou Q, Chen HY, Lei LZ, Qin J, Wang D, Mok VCT, Shi L, Heng P-A (2016) Automatic detection of cerebral microbleeds from MR images via 3D convolutional neural networks. IEEE Trans Med Imaging 35(5):1182–1195

    Article  Google Scholar 

  12. Maier O, Schröder C, Forkert ND, Martinetz T, Handels H (2015) Classifiers for ischemic stroke lesion segmentation: a comparison study. PLoS ONE 10(12):e0145118

    Article  Google Scholar 

  13. Akkus Z, Ali I Sedlar J, Kline TL, Agrawal JP, Parney IF, Giannini C, Erickson BJ (2016) Predicting 1p19q chromosomal deletion of low-grade gliomas from mr images using deep learning. arXiv preprint. arXiv:1611.06939

  14. Feng X, Tustison NJ, Patel SH, Meyer CH (2020) Brain tumor segmentation using an ensemble of 3D U-Nets and overall survival prediction using radiomic features. Front Comput Neurosci 14:25

    Article  Google Scholar 

  15. Anaraki AK, Ayati M, Kazemi F (2019) Magnetic resonance imaging-based brain tumor grades classification and grading via convolutional neural networks and genetic algorithms. Biocybern Biomed Eng 39(1):63–74

    Article  Google Scholar 

  16. Özyurt F, Sert E, Avci E, Dogantekin E (2019) Brain tumor detection based on convolutional neural network with neutrosophic expert maximum fuzzy sure entropy. Measurement 147:106830

    Article  Google Scholar 

  17. Dolz J, Desrosiers C, Ayed IB (2018) IVD-Net: Intervertebral disc localization and segmentation in MRI with a multi-modal UNET. In: International workshop and challenge on computational methods and clinical applications for spine imaging, pp 130–143. Springer, pp 130–143

  18. Lachinov D, Vasiliev E, Turlapov (2018) Glioma segmentation with cascaded UNET. In: International MICCAI Brainlesion workshop. Springer, pp 189–198

  19. Hwang H, Ur Rehman HZ, Lee S (2019) 3D U-Net for skull stripping in brain MRI. Appl Sci 9(3):569

    Article  Google Scholar 

  20. Kingma DP, Ba J (2014) Adam: a method for stochastic optimization. arXiv preprint. arXiv:1412.6980

  21. Mazurowski MA, Clark K, Czarnek NM, Shamsesfandabadi P, Peters KB, Saha A (2017) Radiogenomics of lower-grade glioma: algorithmically-assessed tumor shape is associated with tumor genomic subtypes and patient outcomes in a multi-institutional study with the cancer genome atlas data. J Neuro-Oncol 133(1):27–35

    Article  CAS  Google Scholar 

  22. Zhao L, Jia K (2015) Deep feature learning with discrimination mechanism for brain tumor segmentation and diagnosis. In: 2015 international conference on intelligent information hiding and multimedia signal processing (IIH-MSP). IEEE, pp 306–309

Download references

Funding

None.

Author information

Authors and Affiliations

Authors

Contributions

SG: Conceptualization, methodology and software; AC: Methodology and visualization; and KCS: Supervision, conceptualization, methodology, writing, reviewing and editing.

Corresponding author

Correspondence to KC Santosh.

Ethics declarations

Conflicts of interest

The authors declared that they have no conflict of interest.

Ethical approval

This article does not contain any studies with human participants performed by any of the authors.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Ghosh, S., Chaki, A. & Santosh, K. Improved U-Net architecture with VGG-16 for brain tumor segmentation. Phys Eng Sci Med 44, 703–712 (2021). https://doi.org/10.1007/s13246-021-01019-w

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s13246-021-01019-w

Keywords

Navigation