2023-06-04-hu23a.md

title	booktitle	year	volume	series	month	publisher	pdf	url	abstract	layout	issn	id	tex_title	firstpage	lastpage	page	order	cycles	bibtex_editor	editor	bibtex_author	author	date	address	container-title	genre	issued	extras
Cell Segmenter: A General Framework for Multi-modality Cell Segmentation	Proceedings of the NeurIPS Challenge on Cell Segmentation in Muliti-modality Microscopy Images	2022	212	Proceedings of Machine Learning Research	0	PMLR	https://proceedings.mlr.press/v212/hu23a/hu23a.pdf	https://proceedings.mlr.press/212/hu22.html	Cell Segmentation is an initial and fundamental step in biomedical image analysis, which strongly affects the experimental results of this analysis. Recently, deep learning based segmentation methods have shown great power in segmentation accuracy and efficiency. However, these data-driven methods still face many challenges, such as lack of annotations, multi-modality, and complex morphology, where morphological complexity significantly limits model performance. In this paper, we propose a new all-purpose framework with high morphological adaptability for multi-modality cell segmentation, termed Cell Segmenter (CS). For high convex cells with an arbitrary size, the Anchor-based Watershed Framework (AWF) precisely locates well-defined cell centers and generates segmentation based on these markers. For those elongated or non-convex cells, the center-independent segmentation method Omnipose is adopted to obtain satisfying masks. In the inference time, confidence-based quality estimation is conducted on the branch predictions if needed, and then the better result is chosen as the final segmentation. The F1-score of the proposed method reaches 0.8537 on TuningSet and 0.6216 on the final test set of the NeurIPS 2022 Cell Segmentation Challenge.	inproceedings	2640-3498	hu23a	Cell Segmenter: A General Framework for Multi-modality Cell Segmentation	1	12	1-12	1	false	Ma, Jun and Xie, Ronald and Gupta, Anubha and Guilherme de Almeida, Jos\'e and Bader, Gary D. and Wang, Bo	given family Jun Ma given family Ronald Xie given family Anubha Gupta given family prefix José Almeida Guilherme de given family Gary D. Bader given family Bo Wang	Hu, Kaiwen and Zhang, Shengxuming and Jia, Zhijie and Cheng, Lechao and Zunlei, Feng	given family Kaiwen Hu given family Shengxuming Zhang given family Zhijie Jia given family Lechao Cheng given family Feng Zunlei	2023-06-04		Proceedings of The Cell Segmentation Challenge in Multi-modality High-Resolution Microscopy Images	inproceedings	date-parts 2023 6 4