Weakly supervised cell instance segmentation under various conditions

Kazuya Nishimura, Chenyang Wang, Kazuhide Watanabe, Dai Fei Elmer Ker, Ryoma Bise

Research output: Contribution to journalArticlepeer-review

17 Citations (Scopus)


Cell instance segmentation is important in biomedical research. For living cell analysis, microscopy images are captured under various conditions (e.g., the type of microscopy and type of cell). Deep-learning-based methods can be used to perform instance segmentation if sufficient annotations of individual cell boundaries are prepared as training data. Generally, annotations are required for each condition, which is very time-consuming and labor-intensive. To reduce the annotation cost, we propose a weakly supervised cell instance segmentation method that can segment individual cell regions under various conditions by only using rough cell centroid positions as training data. This method dramatically reduces the annotation cost compared with the standard annotation method of supervised segmentation. We demonstrated the efficacy of our method on various cell images; it outperformed several of the conventional weakly-supervised methods on average. In addition, we demonstrated that our method can perform instance cell segmentation without any manual annotation by using pairs of phase contrast and fluorescence images in which cell nuclei are stained as training data.

Original languageEnglish
Article number102182
JournalMedical Image Analysis
Publication statusPublished - Oct 2021

All Science Journal Classification (ASJC) codes

  • Radiological and Ultrasound Technology
  • Radiology Nuclear Medicine and imaging
  • Computer Vision and Pattern Recognition
  • Health Informatics
  • Computer Graphics and Computer-Aided Design


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