Journal
IMAGE ANALYSIS & STEREOLOGY
Volume 40, Issue 1, Pages 3-16Publisher
INT SOC STEREOLOGY
DOI: 10.5566/ias.2432
Keywords
discrete wavelet transform; Fiji plugin; image filtration; structured illumination microscopy
Categories
Funding
- Ministry of Education, Youth and Sports of the Czech Republic [LM2018129, CZ.02.1.01/0.0/0.0/16_013/0001775, CZ.2.16/3.1.00/21547, LO1419]
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This article proposes using discrete wavelet transform (DWT) for filtering super-resolved microscopic images, addressing the issue of potential resolution loss with traditional filtration techniques. The newly developed plugin in the Fiji software package demonstrates the important applications of DWT in image processing.
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.
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