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Tomographic image reconstruction with deep learning is an emerging field, but a recent landmark study reveals that several deep reconstruction networks are unstable for computed tomography (CT) and magnetic resonance imaging (MRI). Specifically, three kinds of instabilities were reported: (1) strong image artefacts from tiny perturbations, (2) small features missing in a deeply reconstructed image, and (3) decreased imaging performance with increased input data. On the other hand, compressed sensing (CS) inspired reconstruction methods do not suffer from these instabilities because of their built-in kernel awareness. For deep reconstruction to realize its full potential and become a mainstream approach for tomographic imaging, it is thus critically important to meet this challenge by stabilizing deep reconstruction networks. Here we propose an Analytic Compressed Iterative Deep (ACID) framework to address this challenge. ACID synergizes a deep reconstruction network trained on big data, kernel awareness from CS-inspired processing, and iterative refinement to minimize the data residual relative to real measurement. Our study demonstrates that the deep reconstruction using ACID is accurate and stable, and sheds light on the converging mechanism of the ACID iteration under a Bounded Relative Error Norm (BREN) condition. In particular, the study shows that ACID-based reconstruction is resilient against adversarial attacks, superior to classic sparsity-regularized reconstruction alone, and eliminates the three kinds of instabilities. We anticipate that this integrative data-driven approach will help promote development and translation of deep tomographic image reconstruction networks into clinical applications.
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The need for tomographic reconstruction from sparse measurements arises when the measurement process is potentially harmful, needs to be rapid, or is uneconomical. In such cases, information from previous longitudinal scans of the same object helps to reconstruct the current object while requiring significantly fewer updating measurements. Our work is based on longitudinal data acquisition scenarios where we wish to study new changes that evolve within an object over time, such as in repeated scanning for disease monitoring, or in tomography-guided surgical procedures. While this is easily feasible when measurements are acquired from a large number of projection views, it is challenging when the number of views is limited. If the goal is to track the changes while simultaneously reducing sub-sampling artefacts, we propose (1) acquiring measurements from a small number of views and using a global unweighted prior-based reconstruction. If the goal is to observe details of new changes, we propose (2) acquiring measurements from a moderate number of views and using a more involved reconstruction routine. We show that in the latter case, a weighted technique is necessary in order to prevent the prior from adversely affecting the reconstruction of new structures that are absent in any of the earlier scans. The reconstruction of new regions is safeguarded from the bias of the prior by computing regional weights that moderate the local influence of the priors. We are thus able to effectively reconstruct both the old and the new structures in the test. In addition to testing on simulated data, we have validated the efficacy of our method on real tomographic data. The results demonstrate the use of both unweighted and weighted priors in different scenarios.
Low-dose tomography is highly preferred in medical procedures for its reduced radiation risk when compared to standard-dose Computed Tomography (CT). However, the lower the intensity of X-rays, the higher the acquisition noise and hence the reconstructions suffer from artefacts. A large body of work has focussed on improving the algorithms to minimize these artefacts. In this work, we propose two new techniques, rescaled non-linear least squares and Poisson-Gaussian convolution, that reconstruct the underlying image making use of an accurate or near-accurate statistical model of the noise in the projections. We also propose a reconstruction method when prior knowledge of the underlying object is available in the form of templates. This is applicable to longitudinal studies wherein the same object is scanned multiple times to observe the changes that evolve in it over time. Our results on 3D data show that prior information can be used to compensate for the low-dose artefacts, and we demonstrate that it is possible to simultaneously prevent the prior from adversely biasing the reconstructions of new changes in the test object, via a method called ``re-irradiation. Additionally, we also present two techniques for automated tuning of the regularization parameters for tomographic inversion.
Recently, deep learning approaches have become the main research frontier for biological image reconstruction problems thanks to their high performance, along with their ultra-fast reconstruction times. However, due to the difficulty of obtaining matched reference data for supervised learning, there has been increasing interest in unsupervised learning approaches that do not need paired reference data. In particular, self-supervised learning and generative models have been successfully used for various biological imaging applications. In this paper, we overview these approaches from a coherent perspective in the context of classical inverse problems, and discuss their applications to biological imaging.
Breast CT provides image volumes with isotropic resolution in high contrast, enabling detection of small calcification (down to a few hundred microns in size) and subtle density differences. Since breast is sensitive to x-ray radiation, dose reduction of breast CT is an important topic, and for this purpose, few-view scanning is a main approach. In this article, we propose a Deep Efficient End-to-end Reconstruction (DEER) network for few-view breast CT image reconstruction. The major merits of our network include high dose efficiency, excellent image quality, and low model complexity. By the design, the proposed network can learn the reconstruction process with as few as O(N) parameters, where N is the side length of an image to be reconstructed, which represents orders of magnitude improvements relative to the state-of-the-art deep-learning-based reconstruction methods that map raw data to tomographic images directly. Also, validated on a cone-beam breast CT dataset prepared by Koning Corporation on a commercial scanner, our method demonstrates a competitive performance over the state-of-the-art reconstruction networks in terms of image quality. The source code of this paper is available at: https://github.com/HuidongXie/DEER.
Retrospectively gated cine (retro-cine) MRI is the clinical standard for cardiac functional analysis. Deep learning (DL) based methods have been proposed for the reconstruction of highly undersampled MRI data and show superior image quality and magnitude faster reconstruction time than CS-based methods. Nevertheless, it remains unclear whether DL reconstruction is suitable for cardiac function analysis. To address this question, in this study we evaluate and compare the cardiac functional values (EDV, ESV and EF for LV and RV, respectively) obtained from highly accelerated MRI acquisition using DL based reconstruction algorithm (DL-cine) with values from CS-cine and conventional retro-cine. To the best of our knowledge, this is the first work to evaluate the cine MRI with deep learning reconstruction for cardiac function analysis and compare it with other conventional methods. The cardiac functional values obtained from cine MRI with deep learning reconstruction are consistent with values from clinical standard retro-cine MRI.
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