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Register a new userLearned backprojection for sparse and limited view photoacoustic tomography
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Added by
Johannes Schwab
Publication date
2019
fields
Electronic Engineering
and research's language is
English
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Filtered backprojection (FBP) is an efficient and popular class of tomographic image reconstruction methods. In photoacoustic tomography, these algorithms are based on theoretically exact analytic inversion formulas which results in accurate reconstructions. However, photoacoustic measurement data are often incomplete (limited detection view and sparse sampling), which results in artefacts in the images reconstructed with FBP. In addition to that, properties such as directivity of the acoustic detectors are not accounted for in standard FBP, which affects the reconstruction quality, too. To account for these issues, in this papers we propose to improve FBP algorithms based on machine learning techniques. In the proposed method, we include additional weight factors in the FBP, that are optimized on a set of incomplete data and the corresponding ground truth photoacoustic source. Numerical tests show that the learned FBP improves the reconstruction quality compared to the standard FBP.
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Many imaging technologies rely on tomographic reconstruction, which requires solving a multidimensional inverse problem given a finite number of projections. Backprojection is a popular class of algorithm for tomographic reconstruction, however it typically results in poor image reconstructions when the projection angles are sparse and/or if the sensors characteristics are not uniform. Several deep learning based algorithms have been developed to solve this inverse problem and reconstruct the image using a limited number of projections. However these algorithms typically require examples of the ground-truth (i.e. examples of reconstructed images) to yield good performance. In this paper, we introduce an unsupervised sparse-view backprojection algorithm, which does not require ground-truth. The algorithm consists of two modules in a generator-projector framework; a convolutional neural network and a spatial transformer network. We evaluated our algorithm using computed tomography (CT) images of the human chest. We show that our algorithm significantly out-performs filtered backprojection when the projection angles are very sparse, as well as when the sensor characteristics vary for different angles. Our approach has practical applications for medical imaging and other imaging modalities (e.g. radar) where sparse and/or non-uniform projections may be acquired due to time or sampling constraints.
Inverse problems spanning four or more dimensions such as space, time and other independent parameters have become increasingly important. State-of-the-art 4D reconstruction methods use model based iterative reconstruction (MBIR), but depend critically on the quality of the prior modeling. Recently, plug-and-play (PnP) methods have been shown to be an effective way to incorporate advanced prior models using state-of-the-art denoising algorithms. However, state-of-the-art denoisers such as BM4D and deep convolutional neural networks (CNNs) are primarily available for 2D or 3D images and extending them to higher dimensions is difficult due to algorithmic complexity and the increased difficulty of effective training. In this paper, we present multi-slice fusion, a novel algorithm for 4D reconstruction, based on the fusion of multiple low-dimensional denoisers. Our approach uses multi-agent consensus equilibrium (MACE), an extension of plug-and-play, as a framework for integrating the multiple lower-dimensional models. We apply our method to 4D cone-beam X-ray CT reconstruction for non destructive evaluation (NDE) of samples that are dynamically moving during acquisition. We implement multi-slice fusion on distributed, heterogeneous clusters in order to reconstruct large 4D volumes in reasonable time and demonstrate the inherent parallelizable nature of the algorithm. We present simulated and real experimental results on sparse-view and limited-angle CT data to demonstrate that multi-slice fusion can substantially improve the quality of reconstructions relative to traditional methods, while also being practical to implement and train.
We investigate the reconstruction problem of limited angle tomography. Such problems arise naturally in applications like digital breast tomosynthesis, dental tomography, electron microscopy etc. Since the acquired tomographic data is highly incomplete, the reconstruction problem is severely ill-posed and the traditional reconstruction methods, such as filtered backprojection (FBP), do not perform well in such situations. To stabilize the reconstruction procedure additional prior knowledge about the unknown object has to be integrated into the reconstruction process. In this work, we propose the use of the sparse regularization technique in combination with curvelets. We argue that this technique gives rise to an edge-preserving reconstruction. Moreover, we show that the dimension of the problem can be significantly reduced in the curvelet domain. To this end, we give a characterization of the kernel of limited angle Radon transform in terms of curvelets and derive a characterization of solutions obtained through curvelet sparse regularization. In numerical experiments, we will present the practical relevance of these results.
Fast image reconstruction techniques are becoming important with the increasing number of scientific cases in high resolution micro and nano tomography. The processing of the large scale three-dimensional data demands new mathematical tools for the tomographic reconstruction task because of the big computational complexity of most current algorithms as the sizes of tomographic data grow with the development of more powerful acquisition hardware and more refined scientific needs. In the present paper we propose a new fast back-projection operator for the processing of tomographic data and compare it against other fast reconstruction techniques.
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 $2.55 times 10^{-3}$ {mu}m$^{-1}$ in the FBP reconstruction to $1.21 times 10^{-3}$ {mu}m$^{-1}$ 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 $1.16 times 10^{-3}$ {mu}m$^{-1}$ 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.
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