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The walevet-based denoising of images in fiji, with exampleapplications in structured illumination microscopy
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SYSNO ASEP 0542949 Document Type J - Journal Article R&D Document Type Journal Article Subsidiary J Článek ve WOS Title The walevet-based denoising of images in fiji, with exampleapplications in structured illumination microscopy Author(s) Čapek, Martin (UMG-J)
Blažíková, Michaela (UMG-J)
Novotný, Ivan (UMG-J)
Chmelová, Helena (UMG-J)
Svoboda, D. (CZ)
Radochová, B. (CZ)
Janáček, J. (CZ)
Horváth, Ondřej (UMG-J)Number of authors 8 Source Title Image Analysis and Stereology. - : Društvo za stereologijo in kvantitativno analizo slike - ISSN 1580-3139
Roč. 40, č. 1 (2021), s. 3-16Number of pages 14 s. Publication form Online - E Language eng - English Country SK - Slovakia Keywords discrete wavelet transform ; Fiji plugin ; image filtration ; structured illumination microscopy Subject RIV BD - Theory of Information OECD category Computer hardware and architecture R&D Projects LM2018129 GA MŠMT - Ministry of Education, Youth and Sports (MEYS) EF16_013/0001775 GA MŠMT - Ministry of Education, Youth and Sports (MEYS) LO1419 GA MŠMT - Ministry of Education, Youth and Sports (MEYS) Method of publishing Limited access Institutional support UMG-J - RVO:68378050 UT WOS 000639563600002 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 Molecular Genetics Contact Nikol Škňouřilová, nikol.sknourilova@img.cas.cz, Tel.: 241 063 217 Year of Publishing 2022 Electronic address https://www.ias-iss.org/ojs/IAS/article/view/2432
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