The Wavelet-Based Denoising Of Images in Fiji, With Example
Applications in Structured Illumination Microscopy

J 2021

The Wavelet-Based Denoising Of Images in Fiji, With Example Applications in Structured Illumination Microscopy

ČAPEK, Martin, Michaela BLAŽÍKOVÁ, Ivan NOVOTNÝ, Helena CHMELOVÁ, David SVOBODA et. al.

Základní údaje

Originální název

The Wavelet-Based Denoising Of Images in Fiji, With Example Applications in Structured Illumination Microscopy

Autoři

ČAPEK, Martin (203 Česká republika), Michaela BLAŽÍKOVÁ (203 Česká republika), Ivan NOVOTNÝ (203 Česká republika), Helena CHMELOVÁ (203 Česká republika), David SVOBODA (203 Česká republika, garant, domácí), Barbora RADOCHOVÁ (203 Česká republika), Jiří JANÁČEK (203 Česká republika) a Ondrej HORVÁTH

Vydání

Image Analysis & Stereology, International Society for Stereology & Image Analysis, 2021, 1580-3139

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10201 Computer sciences, information science, bioinformatics

Stát vydavatele

Slovinsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 0.683

Kód RIV

RIV/00216224:14330/21:00121362

Organizační jednotka

Fakulta informatiky

DOI

http://dx.doi.org/10.5566/ias.2432

UT WoS

000639563600002

Klíčová slova anglicky

discrete wavelet transform; Fiji plugin; image filtration; structured illumination microscopy

Štítky

cbia-web, wavelets

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 10. 6. 2021 22:19, doc. RNDr. David Svoboda, Ph.D.

Anotace

V originále

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.

Návaznosti

EF16_013/0001775, projekt VaV

Název: Modernizace a podpora výzkumných aktivit národní infrastruktury pro biologické a medicínské zobrazování Czech-BioImaging

Citovat

ČAPEK, Martin, Michaela BLAŽÍKOVÁ, Ivan NOVOTNÝ, Helena CHMELOVÁ, David SVOBODA, Barbora RADOCHOVÁ, Jiří JANÁČEK a Ondrej HORVÁTH. The Wavelet-Based Denoising Of Images in Fiji, With Example Applications in Structured Illumination Microscopy. Image Analysis & Stereology. International Society for Stereology & Image Analysis, 2021, roč. 40, č. 1, s. 3-16. ISSN 1580-3139. Dostupné z: https://dx.doi.org/10.5566/ias.2432.

@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 a 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, roč.~40, č.~1, s.~3-16. ISSN~1580-3139. Dostupné z: https://dx.doi.org/10.5566/ias.2432.

Podrobný výpis o publikaci