Limited Angle Tomography for Transmission X-Ray Microscopy Using Deep Learning
This addresses artifact reduction in nano-scale imaging for biology, nanoscience, and materials science, but is incremental as it adapts an existing deep learning method to a new application.
The paper tackles the problem of image reconstruction artifacts in transmission X-ray microscopy due to limited-angle data, applying deep learning for the first time in this context and achieving significant error reduction, with RMSE dropping from 2.55e-3 to 1.21e-3 μm⁻¹ and SSIM improving from 0.625 to 0.920 on synthetic data.
In transmission X-ray microscopy (TXM) systems, the rotation of a scanned sample might be restricted to a limited angular range to avoid collision to other system parts or high attenuation at certain tilting angles. Image reconstruction from such limited angle data suffers from artifacts due to missing data. In this work, deep learning is applied to limited angle reconstruction in TXMs for the first time. With the challenge to obtain sufficient real data for training, training a deep neural network from synthetic data is investigated. Particularly, the U-Net, the state-of-the-art neural network in biomedical imaging, is trained from synthetic ellipsoid data and multi-category data to reduce artifacts in filtered back-projection (FBP) reconstruction images. The proposed method is evaluated on synthetic data and real scanned chlorella data in $100^\circ$ limited angle tomography. For synthetic test data, the U-Net significantly reduces root-mean-square error (RMSE) from $2.55 \times 10^{-3}$ μm$^{-1}$ in the FBP reconstruction to $1.21 \times 10^{-3}$ μm$^{-1}$ in the U-Net reconstruction, and also improves structural similarity (SSIM) index from 0.625 to 0.920. With penalized weighted least square denoising of measured projections, the RMSE and SSIM are further improved to $1.16 \times 10^{-3}$ μm$^{-1}$ and 0.932, respectively. For real test data, the proposed method remarkably improves the 3-D visualization of the subcellular structures in the chlorella cell, which indicates its important value for nano-scale imaging in biology, nanoscience and materials science.