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@article{1758062,
author = {Čapek, Martin and Blažíková, Michaela and Novotný, Ivan and Chmelová, Helena and Svoboda, David and Radochová, Barbora and Janáček, Jiří and Horváth, Ondrej},
article_number = {1},
doi = {http://dx.doi.org/10.5566/ias.2432},
keywords = {discrete wavelet transform; Fiji plugin; image filtration; structured illumination microscopy},
language = {eng},
issn = {1580-3139},
journal = {Image Analysis & Stereology},
title = {The Wavelet-Based Denoising Of Images in Fiji, With Example Applications in Structured Illumination Microscopy},
url = {https://doi.org/10.5566/ias.2432},
volume = {40},
year = {2021}
}
TY - JOUR
ID - 1758062
AU - Čapek, Martin - Blažíková, Michaela - Novotný, Ivan - Chmelová, Helena - Svoboda, David - Radochová, Barbora - Janáček, Jiří - Horváth, Ondrej
PY - 2021
TI - The Wavelet-Based Denoising Of Images in Fiji, With Example Applications in Structured Illumination Microscopy
JF - Image Analysis & Stereology
VL - 40
IS - 1
SP - 3-16
EP - 3-16
PB - International Society for Stereology & Image Analysis
SN - 15803139
KW - discrete wavelet transform
KW - Fiji plugin
KW - image filtration
KW - structured illumination microscopy
UR - https://doi.org/10.5566/ias.2432
N2 - 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.
ER -
ČAPEK, Martin, Michaela BLAŽÍKOVÁ, Ivan NOVOTNÝ, Helena CHMELOVÁ, David SVOBODA, Barbora RADOCHOVÁ, Jiří JANÁČEK and Ondrej HORVÁTH. The Wavelet-Based Denoising Of Images in Fiji, With Example Applications in Structured Illumination Microscopy. \textit{Image Analysis \&{} Stereology}. International Society for Stereology \&{} Image Analysis, 2021, vol.~40, No~1, p.~3-16. ISSN~1580-3139. Available from: https://dx.doi.org/10.5566/ias.2432.
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