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使用基于注意力的残差神经网络消除光片荧光显微镜中的条纹伪影。

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

作者信息

Wei Zechen, Wu Xiangjun, Tong Wei, Zhang Suhui, Yang Xin, Tian Jie, Hui Hui

机构信息

CAS Key Laboratory of Molecular Imaging, The State Key Laboratory of Management and Control for Complex Systems, Institute of Automation, Beijing 100190, China.

Beijing Key Laboratory of Molecular Imaging, Beijing 100190, China.

出版信息

Biomed Opt Express. 2022 Feb 7;13(3):1292-1311. doi: 10.1364/BOE.448838. eCollection 2022 Mar 1.

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.

摘要

条纹伪影会降低光片荧光显微镜(LSFM)图像的质量。由于位于激发光路中的物体不均匀、高吸收或散射,LSFM图像中会在各个方向和类型上产生条纹伪影,如水平、各向异性或多向异性条纹。这些伪影严重降低了LSFM图像的质量。为了解决这个问题,我们提出了一种基于深度学习的新方法来消除条纹伪影。该方法利用了UNet的编码器 - 解码器结构,并在连续卷积层之间集成了残差块和注意力模块。我们的注意力模块在残差块中实现,以学习有用特征并抑制残差特征。通过生成具有不同类型LSFM图像条纹伪影的三个不同退化数据集,对所提出的网络进行了训练和验证。我们的方法可以有效去除生成的以及实际的、因条纹伪影而失真的LSFM图像中的不同条纹。此外,定量分析和广泛的比较结果表明,对于所有三个生成的数据集,与基于经典图像处理算法和其他强大的基于深度学习的去条纹方法相比,我们的方法表现最佳。因此,我们的方法在LSFM中具有巨大的应用前景,并且其应用可以很容易地扩展到受条纹伪影影响的其他模态重建的图像。

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