Research Papers: Imaging

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

[+] Author Affiliations
Xiao Liang, Yali Zang, Di Dong, Mengjie Fang, Xin Yang, Hui Hui, Jie Tian

Chinese Academy of Sciences, Key Laboratory of Molecular Imaging, No. 95 Zhongguancun East Road, Beijing 100190, China

The State Key Laboratory of Management and Control for Complex Systems, No. 95 Zhongguancun East Road, Beijing 100190, China

University of Chinese Academy of Sciences, No. 80 Zhongguancun East Road, Beijing 100190, China

Liwen Zhang

Chinese Academy of Sciences, Key Laboratory of Molecular Imaging, No. 95 Zhongguancun East Road, Beijing 100190, China

The State Key Laboratory of Management and Control for Complex Systems, No. 95 Zhongguancun East Road, Beijing 100190, China

Alicia Arranz

Center for Molecular Biology “Severo Ochoa”, Calle Nicolás Cabrera, 1, Madrid 28049, Spain

Jorge Ripoll

Universidad Carlos III of Madrid, Department of Bioengineering and Aerospace Engineering, Escuela Politécnica Superior, Avd. de la Universidad, 30, Madrid 28911, Spain

Instituto de Investigación Sanitaria del Hospital Gregorio Marañón, Experimental Medicine and Surgery Unit, Calle del Dr. Esquerdo, 46, Madrid 28007, Spain

J. Biomed. Opt. 21(10), 106005 (Oct 26, 2016). doi:10.1117/1.JBO.21.10.106005
History: Received May 31, 2016; Accepted September 28, 2016
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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.

Figures in this Article
© 2016 Society of Photo-Optical Instrumentation Engineers

Citation

Xiao Liang ; Yali Zang ; Di Dong ; Liwen Zhang ; Mengjie Fang, et al.
"Stripe artifact elimination based on nonsubsampled contourlet transform for light sheet fluorescence microscopy", J. Biomed. Opt. 21(10), 106005 (Oct 26, 2016). ; http://dx.doi.org/10.1117/1.JBO.21.10.106005


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