Nuclei Instance Segmentation in Colon Histology Images with YOLOv7

Yıldız S., Memiş A., VARLI S.

2nd International Conference on Advanced Engineering, Technology and Applications, ICAETA 2023, İstanbul, Turkey, 10 - 11 March 2023, vol.1983 CCIS, pp.335-343 identifier

  • Publication Type: Conference Paper / Full Text
  • Volume: 1983 CCIS
  • Doi Number: 10.1007/978-3-031-50920-9_26
  • City: İstanbul
  • Country: Turkey
  • Page Numbers: pp.335-343
  • Keywords: Colon histology images, CoNIC 2022 dataset, Nuclei instance segmentation, Nuclei segmentation, YOLOv7
  • Yıldız Technical University Affiliated: Yes


In histology image analysis, instance-based nuclei segmentation is one of the challenging tasks within the segmentation-guided studies since it is quite troublesome to detect each distinct nuclei instance of each nuclei type in images in contrast to the semantic segmentation in which all the image pixels of a nuclei type are labelled with the same mask ID although the segmented region may comprise of multiple instances. In this paper, an instance-based medical image segmentation task is addressed, and in this context, instances of multiple types of nuclei in colon histology images are aimed to be delineated distinctly. For the instance-based segmentation of the nuclei in colon histology images, the YOLOv7 algorithm and its built-in instance segmentation module are utilized. In the experimental studies performed on Colon Nuclei Identification and Counting (CoNIC) Challenge 2022 colon histology image dataset by using a 5-fold cross-validation performance evaluation strategy, nuclei instances belonging to 6 classes as the neutrophil, epithelial, lymphocyte, plasma, eosinophil and connective were segmented. To calculate the overall system accuracy, the quantification metrics of mean average precision (mAP) and mean panoptic quality (mPQ) were measured. In performance evaluations, quite promising accuracy values were obtained. The mAP values of 0.2885 and 0.2903, and mPQ values of 0.1659 and 0.1704 were observed by using the YOLOv7 algorithm. To the best of our knowledge, this is the first nuclei instance segmentation study with YOLOv7.