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VIČAR, T. CHMELÍK, J. JAKUBÍČEK, R. CHMELÍKOVÁ, L. GUMULEC, J. BALVAN, J. PROVAZNÍK, I. KOLÁŘ, R.
Original Title
Self-supervised pretraining for transferable quantitative phase image cell segmentation
Type
journal article in Web of Science
Language
English
Original Abstract
In this paper, a novel U-Net-based method for robust adherent cell segmentation for quantitative phase microscopy image is designed and optimised. We designed and evaluated four specific post-processing pipelines. To increase the transferability to different cell types, non-deep learning transfer with adjustable parameters is used in the post-processing step. Additionally, we proposed a self-supervised pretraining technique using nonlabelled data, which is trained to reconstruct multiple image distortions and improved the segmentation performance from 0.67 to 0.70 of object-wise intersection over union. Moreover, we publish a new dataset of manually labelled images suitable for this task together with the unlabelled data for self-supervised pretraining.
Keywords
cell segmentation, deep learning, transfer learning, self-supervised
Authors
VIČAR, T.; CHMELÍK, J.; JAKUBÍČEK, R.; CHMELÍKOVÁ, L.; GUMULEC, J.; BALVAN, J.; PROVAZNÍK, I.; KOLÁŘ, R.
Released
24. 9. 2021
Publisher
Optica Publishing Group
Location
2010 MASSACHUSETTS AVE NW, WASHINGTON, DC 20036
ISBN
2156-7085
Periodical
Biomedical Optics Express
Year of study
12
Number
10
State
United States of America
Pages from
6514
Pages to
6528
Pages count
15
URL
https://www.osapublishing.org/boe/fulltext.cfm?uri=boe-12-10-6514&id=459853
Full text in the Digital Library
http://hdl.handle.net/11012/201741
BibTex
@article{BUT172596, author="Tomáš {Vičar} and Jiří {Chmelík} and Roman {Jakubíček} and Larisa {Chmelíková} and Jaromír {Gumulec} and Jan {Balvan} and Valentine {Provazník} and Radim {Kolář}", title="Self-supervised pretraining for transferable quantitative phase image cell segmentation", journal="Biomedical Optics Express", year="2021", volume="12", number="10", pages="6514--6528", doi="10.1364/BOE.433212", issn="2156-7085", url="https://www.osapublishing.org/boe/fulltext.cfm?uri=boe-12-10-6514&id=459853" }