Colorectal cancer tumor grade segmentation: A new dataset and baseline results.

Duygu Arslan, Sina Sehlaver, Erce Guder, Mehmet Arda Temena, Alper Bahcekapili, Umut Ozdemir, Duriye Ozer Turkay, Gunes Guner, Servet Guresci, Cenk Sokmensuer, Emre Akbas, Ahmet Acar
Author Information
  1. Duygu Arslan: Middle East Technical University, Department of Electrical and Electronics Engineering, Ankara, 06800, Türkiye.
  2. Sina Sehlaver: Middle East Technical University, Department of Computer Engineering, Ankara, 06800, Türkiye.
  3. Erce Guder: Middle East Technical University, Department of Computer Engineering, Ankara, 06800, Türkiye.
  4. Mehmet Arda Temena: Middle East Technical University, Department of Biological Sciences, Ankara, 06800, Türkiye.
  5. Alper Bahcekapili: Middle East Technical University, Department of Computer Engineering, Ankara, 06800, Türkiye.
  6. Umut Ozdemir: TOBB University of Economics and Technology, Department of Computer Engineering, Ankara, 06560, Türkiye.
  7. Duriye Ozer Turkay: Ministry of Health Ankara Bilkent City Hospital, Department of Pathology, Ankara, 06800, Türkiye.
  8. Gunes Guner: Hacettepe University School of Medicine, Department of Pathology, Ankara, 06100, Türkiye.
  9. Servet Guresci: Ministry of Health Ankara Bilkent City Hospital, Department of Pathology, Ankara, 06800, Türkiye.
  10. Cenk Sokmensuer: Hacettepe University School of Medicine, Department of Pathology, Ankara, 06100, Türkiye.
  11. Emre Akbas: Middle East Technical University, Department of Computer Engineering, Ankara, 06800, Türkiye.
  12. Ahmet Acar: Middle East Technical University, Department of Biological Sciences, Ankara, 06800, Türkiye.

Abstract

Routine pathology assessment for the tumor grading is currently performed under the microscope by experienced pathologists which might be prone to interpersonal variability and requiring years of experience. Over the past decade, with the help of whole-slide scanning technology, it is now possible to generate whole-slide images. Indeed, this provides an opportunity to extract vision-based information latent in these images and automate and assist pathologists in their daily workflow. In this process, key machine learning algorithms have been developed enabling an automatic segmentation of pathology slides. Here, in this study, we present a novel dataset for Colorectal Cancer Tumor Grade Segmentation, which contains a total of 103 whole-slide images. The ground-truth annotations for these images were obtained from two independent pathologists. The annotations include pixelwise segmentation masks for "Grade-1", "Grade-2", "Grade-3" tumor classes, and "Normal-mucosa" for the normal class. To establish baseline results for this dataset, we trained and evaluated prominent convolutional neural network and transformer models. Our results show that SwinT, a transformer-based model, achieves 63 % mean-dice score, outperforming other transformer-based models and all CNN based models, aligning with the recent success of transformer-based models in the field of computer vision. Most importantly, our new dataset addresses the absence of publicly available datasets for tumor segmentation. Taken together, the findings from our study indicate that integrating various deep neural network structures is promising at facilitating a more unbiased and consistent tumor grading of colorectal cancer using a novel dataset which is publicly available to all researchers.

Keywords

References

  1. IEEE Trans Med Imaging. 2000 Mar;19(3):203-10 [PMID: 10875704]
  2. Br J Pharmacol. 2021 Nov;178(21):4291-4315 [PMID: 34302297]
  3. Med Image Anal. 2020 Jul;63:101696 [PMID: 32330851]
  4. IEEE J Biomed Health Inform. 2021 Oct;25(10):3700-3708 [PMID: 33232248]
  5. Histopathology. 1998 Aug;33(2):99-106 [PMID: 9762541]
  6. IEEE Trans Pattern Anal Mach Intell. 2017 Apr;39(4):640-651 [PMID: 27244717]
  7. Front Oncol. 2021 Mar 09;11:638182 [PMID: 33768000]
  8. Nat Rev Clin Oncol. 2019 Nov;16(11):703-715 [PMID: 31399699]
  9. Med Image Anal. 2019 Jul;55:1-14 [PMID: 30991188]
  10. J Clin Pathol. 1983 Apr;36(4):385-91 [PMID: 6833507]
  11. Med Image Anal. 2019 Dec;58:101549 [PMID: 31499320]
  12. CA Cancer J Clin. 2017 Mar;67(2):93-99 [PMID: 28094848]
  13. Med Image Anal. 2021 Jan;67:101854 [PMID: 33091742]
  14. Cell Rep. 2018 Apr 3;23(1):181-193.e7 [PMID: 29617659]
  15. J Digit Imaging. 2021 Feb;34(1):105-115 [PMID: 33169211]
  16. Sensors (Basel). 2021 Aug 09;21(16): [PMID: 34450802]
  17. J Pathol Inform. 2018 Nov 14;9:38 [PMID: 30607305]
  18. Nat Med. 2015 Nov;21(11):1350-6 [PMID: 26457759]
  19. Hepatogastroenterology. 2009 Sep-Oct;56(94-95):1335-40 [PMID: 19950787]
  20. Sci Data. 2022 Sep 27;9(1):588 [PMID: 36167846]
  21. Med Image Anal. 2019 Aug;56:122-139 [PMID: 31226662]
  22. Conf Comput Vis Pattern Recognit Workshops. 2021 Jun;2021:14318-14328 [PMID: 35047230]
  23. CA Cancer J Clin. 2021 May;71(3):209-249 [PMID: 33538338]
  24. IEEE Trans Med Imaging. 2022 Mar;41(3):702-714 [PMID: 34705638]
  25. Nat Med. 2021 May;27(5):775-784 [PMID: 33990804]
  26. Sci Rep. 2023 May 24;13(1):8398 [PMID: 37225743]
  27. Sci Rep. 2017 Dec 4;7(1):16878 [PMID: 29203879]
  28. Comput Biol Med. 2022 Jul;146:105539 [PMID: 35483227]
  29. Comput Med Imaging Graph. 2021 Mar;88:101866 [PMID: 33485058]
  30. Patterns (N Y). 2023 Feb 10;4(2):100688 [PMID: 36873900]
  31. J Pers Med. 2022 Sep 01;12(9): [PMID: 36143229]
  32. Med Image Anal. 2022 Jan;75:102264 [PMID: 34781160]
  33. Gigascience. 2018 Jun 1;7(6): [PMID: 29860392]
  34. Nat Genet. 2013 Oct;45(10):1113-20 [PMID: 24071849]
  35. CA Cancer J Clin. 2020 May;70(3):145-164 [PMID: 32133645]
  36. Histopathology. 2008 Mar;52(4):494-9 [PMID: 18315602]
  37. Transl Oncol. 2021 Oct;14(10):101174 [PMID: 34243011]

Word Cloud

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