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THE WAVELET-BASED DENOISING OF IMAGES IN FIJI, WITH EXAMPLE APPLICATIONS IN STRUCTURED ILLUMINATION MICROSCOPY

SYSNO ASEP	0542439
Document Type	J - Journal Article
R&D Document Type	Journal Article
Subsidiary J	Článek ve WOS
Title	THE WAVELET-BASED DENOISING OF IMAGES IN FIJI, WITH EXAMPLE APPLICATIONS IN STRUCTURED ILLUMINATION MICROSCOPY
Author(s)	Čapek, Martin (FGU-C)_{RID, ORCID} Blažíková, M. (CZ) Novotný, I. (CZ) Chmelová, H. (CZ) Svoboda, D. (CZ) Radochová, Barbora (FGU-C)_{RID, ORCID} Janáček, Jiří (FGU-C)_{RID, ORCID} Horváth, O. (CZ)
Source Title	Image Analysis and Stereology. - : Društvo za stereologijo in kvantitativno analizo slike - ISSN 1580-3139 Roč. 40, č. 1 (2021), s. 3-16
Number of pages	14 s.
Language	eng - English
Country	SI - Slovenia
Keywords	discrete wavelet transform ; Fiji plugin ; image filtration ; structured illumination microscopy
Subject RIV	BD - Theory of Information
OECD category	Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)
R&D Projects	EF16_013/0001775 GA MŠMT - Ministry of Education, Youth and Sports (MEYS)
	LM2018129 GA MŠMT - Ministry of Education, Youth and Sports (MEYS)
Method of publishing	Open access
Institutional support	FGU-C - RVO:67985823
UT WOS	000639563600002
EID SCOPUS	85111492312
DOI	10.5566/ias.2432
Annotation	Filtration of super-resolved microscopic images brings often troubles with removing undesired image parts like, e.g., noise, inhomogenous background and reconstruction artifacts. Standard filtration techniques, e.g., convolution- or Fourier transform-based methods are not always appropriate, since they may lower image resolution that was acquired by hi-tech and expensive microscopy systems. Thus, in this article it is proposed to filter such images using discrete wavelet transform (DWT). Newly developed Wavelet_Denoise plugin for free available Fiji software package demonstrates important possibilities of applying DWT to images: Decomposition of a filtered picture using various wavelet filters and levels of details with showing decomposed images and visualization of effects of back transformation of the picture with chosen level of suppression or denoising of wavelet coefficients. The Fiji framework allows, for example, using a plethora of various microscopic image formats for data opening, users can easily install the plugin through a menu command and the plugin supports processing 3D images in Z-stacks. The application of the plugin for removal of reconstruction artifacts and undesirable background in images acquired by super-resolved structured illumination microscopy is demonstrated as well.
Workplace	Institute of Physiology
Contact	Lucie Trajhanová, lucie.trajhanova@fgu.cas.cz, Tel.: 241 062 400
Year of Publishing	2022
Electronic address	https://www.ias-iss.org/ojs/IAS/article/view/2432

Number of the records: 1