Elimination of stripe artifacts in light sheet fluorescence microscopy using an attention-based residual neural network

Abstract

Stripe artifacts can deteriorate the quality of light sheet fluorescence microscopy (LSFM) images. Owing to the inhomogeneous, high-absorption, or scattering objects located in the excitation light path, stripe artifacts are generated in LSFM images in various directions and types, such as horizontal, anisotropic, or multidirectional anisotropic. These artifacts severely degrade the quality of LSFM images. To address this issue, we proposed a new deep-learning-based approach for the elimination of stripe artifacts. This method utilizes an encoder–decoder structure of UNet integrated with residual blocks and attention modules between successive convolutional layers. Our attention module was implemented in the residual blocks to learn useful features and suppress the residual features. The proposed network was trained and validated by generating three different degradation datasets with different types of stripe artifacts in LSFM images. Our method can effectively remove different stripes in generated and actual LSFM images distorted by stripe artifacts. Besides, quantitative analysis and extensive comparison results demonstrated that our method performs the best compared with classical image-based processing algorithms and other powerful deep-learning-based destriping methods for all three generated datasets. Thus, our method has tremendous application prospects to LSFM, and its use can be easily extended to images reconstructed by other modalities affected by the presence of stripe artifacts.