TVCondNet: A Conditional Denoising Neural Network for NMR Spectroscopy

Nuclear Magnetic Resonance (NMR) spectroscopy is a widely-used technique in the fields of bio-medicine, chemistry, and biology for the analysis of chemicals and proteins. The signals from NMR spectroscopy often have low signal-to-noise ratio (SNR) due to acquisition noise, which poses significant challenges for subsequent analysis. Recent work has explored the potential of deep learning (DL) for NMR denoising, showing significant performance gains over traditional methods such as total variation (TV) denoising. This paper shows that the performance of DL denoising for NMR can be further improved by combining data-driven training with traditional TV denoising. The proposed TVCondNet method outperforms both traditional TV and DL methods by including the TV solution as a condition during DL training. Our validation on experimentally collected NMR data shows the superior denoising performance and faster inference speed of TVCondNet compared to existing methods.

Pseudo-MRI-Guided PET Image Reconstruction Method Based on a Diffusion Probabilistic Model

Anatomically guided PET reconstruction using MRI information has been shown to have the potential to improve PET image quality. However, these improvements are limited to PET scans with paired MRI information. In this work we employed a diffusion probabilistic model (DPM) to infer T1-weighted-MRI (deep-MRI) images from FDG-PET brain images. We then use the DPM-generated T1w-MRI to guide the PET reconstruction. The model was trained with brain FDG scans, and tested in datasets containing multiple levels of counts. Deep-MRI images appeared somewhat degraded than the acquired MRI images. Regarding PET image quality, volume of interest analysis in different brain regions showed that both PET reconstructed images using the acquired and the deep-MRI images improved image quality compared to OSEM. Same conclusions were found analysing the decimated datasets. A subjective evaluation performed by two physicians confirmed that OSEM scored consistently worse than the MRI-guided PET images and no significant differences were observed between the MRI-guided PET images. This proof of concept shows that it is possible to infer DPM-based MRI imagery to guide the PET reconstruction, enabling the possibility of changing reconstruction parameters such as the strength of the prior on anatomically guided PET reconstruction in the absence of MRI.

PnP Restoration with Domain Adaptation for SANS

Small Angle Neutron Scattering (SANS) is a non-destructive technique utilized to probe the nano- to mesoscale structure of materials by analyzing the scattering pattern of neutrons. Accelerating SANS acquisition for in-situ analysis is essential, but it often reduces the signal-to-noise ratio (SNR), highlighting the need for methods to enhance SNR even with short acquisition times. While deep learning (DL) can be used for enhancing SNR of low quality SANS, the amount of experimental data available for training is usually severely limited. We address this issue by proposing a Plug-and-play Restoration for SANS (PR-SANS) that uses domain-adapted priors. The prior in PR-SANS is initially trained on a set of generic images and subsequently fine-tuned using a limited amount of experimental SANS data. We present a theoretical convergence analysis of PR-SANS by focusing on the error resulting from using inexact domain-adapted priors instead of the ideal ones. We demonstrate with experimentally collected SANS data that PR-SANS can recover high-SNR 2D SANS detector images from low-SNR detector images, effectively increasing the SNR. This advancement enables a reduction in acquisition times by a factor of 12 while maintaining the original signal quality.

Overcoming Distribution Shifts in Plug-and-Play Methods with Test-Time Training

Plug-and-Play Priors (PnP) is a well-known class of methods for solving inverse problems in computational imaging. PnP methods combine physical forward models with learned prior models specified as image denoisers. A common issue with the learned models is that of a performance drop when there is a distribution shift between the training and testing data. Test-time training (TTT) was recently proposed as a general strategy for improving the performance of learned models when training and testing data come from different distributions. In this paper, we propose PnP-TTT as a new method for overcoming distribution shifts in PnP. PnP-TTT uses deep equilibrium learning (DEQ) for optimizing a self-supervised loss at the fixed points of PnP iterations. PnP-TTT can be directly applied on a single test sample to improve the generalization of PnP. We show through simulations that given a sufficient number of measurements, PnP-TTT enables the use of image priors trained on natural images for image reconstruction in magnetic resonance imaging (MRI).

Convergence of Nonconvex PnP-ADMM with MMSE Denoisers

Plug-and-Play Alternating Direction Method of Multipliers (PnP-ADMM) is a widely-used algorithm for solving inverse problems by integrating physical measurement models and convolutional neural network (CNN) priors. PnP-ADMM has been theoretically proven to converge for convex data-fidelity terms and nonexpansive CNNs. It has however been observed that PnP-ADMM often empirically converges even for expansive CNNs. This paper presents a theoretical explanation for the observed stability of PnP-ADMM based on the interpretation of the CNN prior as a minimum mean-squared error (MMSE) denoiser. Our explanation parallels a similar argument recently made for the iterative shrinkage/thresholding algorithm variant of PnP (PnP-ISTA) and relies on the connection between MMSE denoisers and proximal operators. We also numerically evaluate the performance gap between PnP-ADMM using a nonexpansive DnCNN denoiser and expansive DRUNet denoiser, thus motivating the use of expansive CNNs.

DiffGEPCI: 3D MRI Synthesis from mGRE Signals using 2.5D Diffusion Model

We introduce a new framework called DiffGEPCI for cross-modality generation in magnetic resonance imaging (MRI) using a 2.5D conditional diffusion model. DiffGEPCI can synthesize high-quality Fluid Attenuated Inversion Recovery (FLAIR) and Magnetization Prepared-Rapid Gradient Echo (MPRAGE) images, without acquiring corresponding measurements, by leveraging multi-Gradient-Recalled Echo (mGRE) MRI signals as conditional inputs. DiffGEPCI operates in a two-step fashion: it initially estimates a 3D volume slice-by-slice using the axial plane and subsequently applies a refinement algorithm (referred to as 2.5D) to enhance the quality of the coronal and sagittal planes. Experimental validation on real mGRE data shows that DiffGEPCI achieves excellent performance, surpassing generative adversarial networks (GANs) and traditional diffusion models.

FLAIR: A Conditional Diffusion Framework with Applications to Face Video Restoration

Face video restoration (FVR) is a challenging but important problem where one seeks to recover a perceptually realistic face videos from a low-quality input. While diffusion probabilistic models (DPMs) have been shown to achieve remarkable performance for face image restoration, they often fail to preserve temporally coherent, high-quality videos, compromising the fidelity of reconstructed faces. We present a new conditional diffusion framework called FLAIR for FVR. FLAIR ensures temporal consistency across frames in a computationally efficient fashion by converting a traditional image DPM into a video DPM. The proposed conversion uses a recurrent video refinement layer and a temporal self-attention at different scales. FLAIR also uses a conditional iterative refinement process to balance the perceptual and distortion quality during inference. This process consists of two key components: a data-consistency module that analytically ensures that the generated video precisely matches its degraded observation and a coarse-to-fine image enhancement module specifically for facial regions. Our extensive experiments show superiority of FLAIR over the current state-of-the-art (SOTA) for video super-resolution, deblurring, JPEG restoration, and space-time frame interpolation on two high-quality face video datasets.

Dose-aware Diffusion Model for 3D Ultra Low-dose PET Imaging

As PET imaging is accompanied by substantial radiation exposure and cancer risk, reducing radiation dose in PET scans is an important topic. Recently, diffusion models have emerged as the new state-of-the-art generative model to generate high-quality samples and have demonstrated strong potential for various tasks in medical imaging. However, it is difficult to extend diffusion models for 3D image reconstructions due to the memory burden. Directly stacking 2D slices together to create 3D image volumes would results in severe inconsistencies between slices. Previous works tried to either applying a penalty term along the z-axis to remove inconsistencies or reconstructing the 3D image volumes with 2 pre-trained perpendicular 2D diffusion models. Nonetheless, these previous methods failed to produce satisfactory results in challenging cases for PET image denoising. In addition to administered dose, the noise-levels in PET images are affected by several other factors in clinical settings, such as scan time, patient size, and weight, etc. Therefore, a method to simultaneously denoise PET images with different noise-levels is needed. Here, we proposed a dose-aware diffusion model for 3D low-dose PET imaging (DDPET) to address these challenges. The proposed DDPET method was tested on 295 patients from three different medical institutions globally with different low-dose levels. These patient data were acquired on three different commercial PET scanners, including Siemens Vision Quadra, Siemens mCT, and United Imaging Healthcare uExplorere. The proposed method demonstrated superior performance over previously proposed diffusion models for 3D imaging problems as well as models proposed for noise-aware medical image denoising. Code is available at: xxx.

A Structured Pruning Algorithm for Model-based Deep Learning

There is a growing interest in model-based deep learning (MBDL) for solving imaging inverse problems. MBDL networks can be seen as iterative algorithms that estimate the desired image using a physical measurement model and a learned image prior specified using a convolutional neural net (CNNs). The iterative nature of MBDL networks increases the test-time computational complexity, which limits their applicability in certain large-scale applications. We address this issue by presenting structured pruning algorithm for model-based deep learning (SPADE) as the first structured pruning algorithm for MBDL networks. SPADE reduces the computational complexity of CNNs used within MBDL networks by pruning its non-essential weights. We propose three distinct strategies to fine-tune the pruned MBDL networks to minimize the performance loss. Each fine-tuning strategy has a unique benefit that depends on the presence of a pre-trained model and a high-quality ground truth. We validate SPADE on two distinct inverse problems, namely compressed sensing MRI and image super-resolution. Our results highlight that MBDL models pruned by SPADE can achieve substantial speed up in testing time while maintaining competitive performance.

PtychoDV: Vision Transformer-Based Deep Unrolling Network for Ptychographic Image Reconstruction

Ptychography is an imaging technique that captures multiple overlapping snapshots of a sample, illuminated coherently by a moving localized probe. The image recovery from ptychographic data is generally achieved via an iterative algorithm that solves a nonlinear phase-field problem derived from measured diffraction patterns. However, these approaches have high computational cost. In this paper, we introduce PtychoDV, a novel deep model-based network designed for efficient, high-quality ptychographic image reconstruction. PtychoDV comprises a vision transformer that generates an initial image from the set of raw measurements, taking into consideration their mutual correlations. This is followed by a deep unrolling network that refines the initial image using learnable convolutional priors and the ptychography measurement model. Experimental results on simulated data demonstrate that PtychoDV is capable of outperforming existing deep learning methods for this problem, and significantly reduces computational cost compared to iterative methodologies, while maintaining competitive performance.