Self-supervised pretraining for transferable quantitative phase image cell segmentation

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Publikace nespadá pod Ústav výpočetní techniky, ale pod Lékařskou fakultu. Oficiální stránka publikace je na webu muni.cz.

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VIČAR Tomáš CHEMELIK Jiri JAKUBICEK Roman CHMELIKOVA Larisa GUMULEC Jaromír BALVAN Jan PROVAZNÍK Ivo KOLAR Radim

Rok publikování 2021
Druh Článek v odborném periodiku
Časopis / Zdroj BIOMEDICAL OPTICS EXPRESS
Fakulta / Pracoviště MU

Lékařská fakulta

Citace
www https://www.osapublishing.org/boe/fulltext.cfm?uri=boe-12-10-6514&id=459853
Doi http://dx.doi.org/10.1364/BOE.433212
Klíčová slova Self-supervised pretraining; transferable quantitative phase image cell segmentation
Popis 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. (c) 2021 Optical Society of America under the terms of the OSA Open Access Publishing Agreement
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