Self-Supervised Deep Unrolled Reconstruction Using Regularization by Denoising.

Deep learning methods have been successfully used in various computer vision tasks. Inspired by that success, deep learning has been explored in magnetic resonance imaging (MRI) reconstruction. In particular, integrating deep learning and model-based optimization methods has shown considerable advantages. However, a large amount of labeled training data is typically needed for high reconstruction quality, which is challenging for some MRI applications. In this paper, we propose a novel reconstruction method, named DURED-Net, that enables interpretable self-supervised learning for MR image reconstruction by combining a self-supervised denoising network and a plug-and-play method. We aim to boost the reconstruction performance of Noise2Noise in MR reconstruction by adding an explicit prior that utilizes imaging physics. Specifically, the leverage of a denoising network for MRI reconstruction is achieved using Regularization by Denoising (RED). Experiment results demonstrate that the proposed method requires a reduced amount of training data to achieve high reconstruction quality among the state-of-the-art approaches utilizing Noise2Noise.

SuperMAP: Deep ultrafast MR relaxometry with joint spatiotemporal undersampling.

PURPOSE: To develop an ultrafast and robust MR parameter mapping network using deep learning. THEORY AND METHODS: We design a deep learning framework called SuperMAP that directly converts a series of undersampled (both in k-space and parameter-space) parameter-weighted images into several quantitative maps, bypassing the conventional exponential fitting procedure. We also present a novel technique to simultaneously reconstruct T1rho and T2 relaxation maps within a single scan. Full data were acquired and retrospectively undersampled for training and testing using traditional and state-of-the-art techniques for comparison. Prospective data were also collected to evaluate the trained network. The performance of all methods is evaluated using the parameter qualification errors and other metrics in the segmented regions of interest. RESULTS: SuperMAP achieved accurate T1rho and T2 mapping with high acceleration factors (R = 24 and R = 32). It exploited both spatial and temporal information and yielded low error (normalized mean square error of 2.7% at R = 24 and 2.8% at R = 32) and high resemblance (structural similarity of 97% at R = 24 and 96% at R = 32) to the gold standard. The network trained with retrospectively undersampled data also works well for the prospective data (with a slightly lower acceleration factor). SuperMAP is also superior to conventional methods. CONCLUSION: Our results demonstrate the feasibility of generating superfast MR parameter maps through very few undersampled parameter-weighted images. SuperMAP can simultaneously generate T1rho and T2 relaxation maps in a short scan time.

Minimizing Molecular Misidentification in Imaging Low-Abundance Protein Interactions Using Spectroscopic Single-Molecule Localization Microscopy.

Super-resolution microscopy can capture spatiotemporal organizations of protein interactions with resolution down to 10 nm; however, the analyses of more than two proteins involving low-abundance protein are challenging because spectral crosstalk and heterogeneities of individual fluorescent labels result in molecular misidentification. Here we developed a deep learning-based imaging analysis method for spectroscopic single-molecule localization microscopy to minimize molecular misidentification in three-color super-resolution imaging. We characterized the 3-fold reduction of molecular misidentification in the new imaging method using pure samples of different photoswitchable fluorophores and visualized three distinct subcellular proteins in U2-OS cell lines. We further validated the protein counts and interactions of TOMM20, DRP1, and SUMO1 in a well-studied biological process, Staurosporine-induced apoptosis, by comparing the imaging results with Western-blot analyses of different subcellular portions.

Diagnostic interchangeability of deep convolutional neural networks reconstructed knee MR images: preliminary experience.

BACKGROUND: MRI acceleration using deep learning (DL) convolutional neural networks (CNNs) is a novel technique with great promise. Increasing the number of convolutional layers may allow for more accurate image reconstruction. Studies on evaluating the diagnostic interchangeability of DL reconstructed knee magnetic resonance (MR) images are scarce. The purpose of this study was to develop a deep CNN (DCNN) with an optimal number of layers for accelerating knee magnetic resonance imaging (MRI) acquisition by 6-fold and to test the diagnostic interchangeability and image quality of nonaccelerated images versus images reconstructed with a 15-layer DCNN or 3-layer CNN. METHODS: For the feasibility portion of this study, 10 patients were randomly selected from the Osteoarthritis Initiative (OAI) cohort. For the interchangeability portion of the study, 40 patients were randomly selected from the OAI cohort. Three readers assessed meniscal and anterior cruciate ligament (ACL) tears and cartilage defects using DCNN, CNN, and nonaccelerated images. Image quality was subjectively graded as nondiagnostic, poor, acceptable, or excellent. Interchangeability was tested by comparing the frequency of agreement when readers used both accelerated and nonaccelerated images to frequency of agreement when readers only used nonaccelerated images. A noninferiority margin of 0.10 was used to ensure type I error ≤5% and power ≥80%. A logistic regression model using generalized estimating equations was used to compare proportions; 95% confidence intervals (CIs) were constructed. RESULTS: DCNN and CNN images were interchangeable with nonaccelerated images for all structures, with excess disagreement values ranging from -2.5% [95% CI: (-6.1, 1.1)] to 3.0% [95% CI: (-0.1, 6.1)]. The quality of DCNN images was graded higher than that of CNN images but less than that of nonaccelerated images [excellent/acceptable quality: DCNN, 95% of cases (114/120); CNN, 60% (72/120); nonaccelerated, 97.5% (117/120)]. CONCLUSIONS: Six-fold accelerated knee images reconstructed with a DL technique are diagnostically interchangeable with nonaccelerated images and have acceptable image quality when using a 15-layer CNN.