An interactive ImageJ plugin for semi-automated image denoising in electron microscopy

被引：39

作者：

Roels, Joris ^{[1
,2
]}

Vernaillen, Frank ^{[3
,4
]}

Kremer, Anna ^{[1
,4
,5
]}

Goncalves, Amanda ^{[1
,4
,5
]}

Aelterman, Jan ^{[6
]}

Luong, Hiep Q. ^{[6
]}

Goossens, Bart ^{[6
]}

Philips, Wilfried ^{[6
]}

Lippens, Saskia ^{[1
,4
,5
]}

Saeys, Yvan ^{[1
,2
]}

机构：

[1] VIB, Ctr Inflammat Res, Technol Pk 71, B-9052 Ghent, Belgium

[2] Univ Ghent, Dept Appl Math Comp Sci & Stat, Krijgslaan 281-S9, B-9000 Ghent, Belgium

[3] VIB, Bioinformat Core, Rijvisschestr 126 3R, B-9052 Ghent, Belgium

[4] VIB, Bioimaging Core, Technol Pk 71, B-9052 Ghent, Belgium

[5] Univ Ghent, Dept Biomed Mol Biol, Technol Pk 71, B-9052 Ghent, Belgium

[6] Univ Ghent, IMEC, Dept Telecommun & Informat Proc, St Pietersnieuwstr 41, B-9000 Ghent, Belgium

来源：

NATURE COMMUNICATIONS | 2020年 / 11卷 / 01期

关键词：

FREQUENCY LOCALIZATION; QUANTITATIVE-ANALYSIS; FILTER; DECONVOLUTION; TRANSFORM; CELL; SEM;

D O I：

10.1038/s41467-020-14529-0

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

The recent advent of 3D in electron microscopy (EM) has allowed for detection of nanometer resolution structures. This has caused an explosion in dataset size, necessitating the development of automated workflows. Moreover, large 3D EM datasets typically require hours to days to be acquired and accelerated imaging typically results in noisy data. Advanced denoising techniques can alleviate this, but tend to be less accessible to the community due to low-level programming environments, complex parameter tuning or a computational bottleneck. We present DenoisEM: an interactive and GPU accelerated denoising plugin for ImageJ that ensures fast parameter tuning and processing through parallel computing. Experimental results show that DenoisEM is one order of magnitude faster than related software and can accelerate data acquisition by a factor of 4 without significantly affecting data quality. Lastly, we show that image denoising benefits visualization and (semi-)automated segmentation and analysis of ultrastructure in various volume EM datasets.

引用

页数：13