Stripe artifact elimination based on nonsubsampled contourlet transform for light sheet fluorescence microscopy

Xiao Liang; Yali Zang; Di Dong; Liwen Zhang; Mengjie Fang; Xin Yang; Alicia Arranz; Jorge Ripoll; Hui Hui; Jie Tian

doi:10.1117/1.JBO.21.10.106005

26 October 2016 Stripe artifact elimination based on nonsubsampled contourlet transform for light sheet fluorescence microscopy

Xiao Liang, Yali Zang, Di Dong, Liwen Zhang, Mengjie Fang, Xin Yang, Alicia Arranz, Jorge Ripoll, Hui Hui, Jie Tian

Author Affiliations +

Funded by: National Basic Research Program of China, National Basic Research Program, National Basic Research Program of China (973 Program), National Natural Science Foundation of China (NSFC), National Natural Science Foundation of China, National Natural Science Foundation, Natural Science Foundation of China, Instrument Developing Project, Strategic Priority Research Program (B), Beijing Municipal Science & Technology Commission, CAS, Beijing Municipal Science and Technology Commission, Beijing Municipal Science and Technology Commission, Marie Curie Intra-European Fellowship Program, Spanish MINECO

Journal of Biomedical Optics, Vol. 21, Issue 10, 106005 (October 2016). https://doi.org/10.1117/1.JBO.21.10.106005

Abstract

Stripe artifacts, caused by high-absorption or high-scattering structures in the illumination light path, are a common drawback in both unidirectional and multidirectional light sheet fluorescence microscopy (LSFM), significantly deteriorating image quality. To circumvent this problem, we present an effective multidirectional stripe remover (MDSR) method based on nonsubsampled contourlet transform (NSCT), which can be used for both unidirectional and multidirectional LSFM. In MDSR, a fast Fourier transform (FFT) filter is designed in the NSCT domain to shrink the stripe components and eliminate the noise. Benefiting from the properties of being multiscale and multidirectional, MDSR succeeds in eliminating stripe artifacts in both unidirectional and multidirectional LSFM. To validate the method, MDSR has been tested on images from a custom-made unidirectional LSFM system and a commercial multidirectional LSFM system, clearly demonstrating that MDSR effectively removes most of the stripe artifacts. Moreover, we performed a comparative experiment with the variational stationary noise remover and the wavelet-FFT methods and quantitatively analyzed the results with a peak signal-to-noise ratio, showing an improved noise removal when using the MDSR method.

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Xiao Liang, Yali Zang, Di Dong, Liwen Zhang, Mengjie Fang, Xin Yang, Alicia Arranz, Jorge Ripoll, Hui Hui, and Jie Tian "Stripe artifact elimination based on nonsubsampled contourlet transform for light sheet fluorescence microscopy," Journal of Biomedical Optics 21(10), 106005 (26 October 2016). https://doi.org/10.1117/1.JBO.21.10.106005

Published: 26 October 2016

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