arXiv subjects

Mengjie Shi

Publications and source records attributed to Mengjie Shi.

5 recordsLinked to original sources

arXiv2024

Learning-based sound speed estimation and aberration correction in linear-array photoacoustic imaging

Photoacoustic (PA) image reconstruction involves acoustic inversion that necessitates the specification of the speed of sound (SoS) within the medium of propagation. Due to the lack of information on the spatial distribution of the SoS within heterogeneous soft tissue, a homogeneous SoS distribution (such as 1540 m/s) is typically assumed in PA image reconstruction, similar to that of ultrasound (US) imaging. Failure to compensate the SoS variations leads to aberration artefacts, deteriorating the image quality. Various methods have been proposed to address this issue, but they usually involve complex hardware and/or time-consuming algorithms, hindering clinical translation. In this work, we introduce a deep learning framework for SoS estimation and subsequent aberration correction in a dual-modal PA/US imaging system exploiting a clinical US probe. As the acquired PA and US images were inherently co-registered, the estimated SoS distribution from US channel data using a deep neural network was incorporated for accurate PA image reconstruction. The framework comprised an initial pre-training stage based on digital phantoms, which was further enhanced through transfer learning using physical phantom data and associated SoS maps obtained from measurements. This framework achieved a root mean square error of 10.2 m/s and 15.2 m/s for SoS estimation on digital and physical phantoms, respectively and structural similarity index measures of up to 0.86 for PA reconstructions as compared to the conventional approach of 0.69. A maximum of 1.2 times improvement in signal-to-noise ratio of PA images was further demonstrated with a human volunteer study. Our results show that the proposed framework could be valuable in various clinical and preclinical applications to enhance PA image reconstruction.

eess.IV↗

arXiv2023

Adversarial Erasing with Pruned Elements: Towards Better Graph Lottery Ticket

Graph Lottery Ticket (GLT), a combination of core subgraph and sparse subnetwork, has been proposed to mitigate the computational cost of deep Graph Neural Networks (GNNs) on large input graphs while preserving original performance. However, the winning GLTs in exisiting studies are obtained by applying iterative magnitude-based pruning (IMP) without re-evaluating and re-considering the pruned information, which disregards the dynamic changes in the significance of edges/weights during graph/model structure pruning, and thus limits the appeal of the winning tickets. In this paper, we formulate a conjecture, i.e., existing overlooked valuable information in the pruned graph connections and model parameters which can be re-grouped into GLT to enhance the final performance. Specifically, we propose an adversarial complementary erasing (ACE) framework to explore the valuable information from the pruned components, thereby developing a more powerful GLT, referred to as the ACE-GLT. The main idea is to mine valuable information from pruned edges/weights after each round of IMP, and employ the ACE technique to refine the GLT processing. Finally, experimental results demonstrate that our ACE-GLT outperforms existing methods for searching GLT in diverse tasks. Our code will be made publicly available.

cs.LG↗

arXiv2022

Improving needle visibility in LED-based photoacoustic imaging using deep learning with semi-synthetic datasets

Photoacoustic imaging has shown great potential for guiding minimally invasive procedures by accurate identification of critical tissue targets and invasive medical devices (such as metallic needles). The use of light emitting diodes (LEDs) as the excitation light sources accelerates its clinical translation owing to its high affordability and portability. However, needle visibility in LED-based photoacoustic imaging is compromised primarily due to its low optical fluence. In this work, we propose a deep learning framework based on U-Net to improve the visibility of clinical metallic needles with a LED-based photoacoustic and ultrasound imaging system. To address the complexity of capturing ground truth for real data and the poor realism of purely simulated data, this framework included the generation of semi-synthetic training datasets combining both simulated data to represent features from the needles and in vivo measurements for tissue background. Evaluation of the trained neural network was performed with needle insertions into blood-vessel-mimicking phantoms, pork joint tissue ex vivo and measurements on human volunteers. This deep learning-based framework substantially improved the needle visibility in photoacoustic imaging in vivo compared to conventional reconstruction by suppressing background noise and image artefacts, achieving 5.8 and 4.5 times improvements in signal-to-noise ratio (SNR) and the modified Hausdorff distance (MHD) respectively. Thus, the proposed framework could be helpful for reducing complications during percutaneous needle insertions by accurate identification of clinical needles in photoacoustic imaging.

eess.IV↗

arXiv2022

Spatiotemporal singular value decomposition for denoising in photoacoustic imaging with low-energy excitation light source

Photoacoustic (PA) imaging is an emerging hybrid imaging modality that combines rich optical spectroscopic contrast and high ultrasonic resolution and thus holds tremendous promise for a wide range of pre-clinical and clinical applications. Compact and affordable light sources such as light-emitting diodes (LEDs) and laser diodes (LDs) are promising alternatives to bulky and expensive solid-state laser systems that are commonly used as PA light sources. These could accelerate the clinical translation of PA technology. However, PA signals generated with these light sources are readily degraded by noise due to the low optical fluence, leading to decreased signal-to-noise ratio (SNR) in PA images. In this work, a spatiotemporal singular value decomposition (SVD) based PA denoising method was investigated for these light sources that usually have low fluence and high repetition rates. The proposed method leverages both spatial and temporal correlations between radiofrequency (RF) data frames. Validation was performed on simulations and in vivo PA data acquired from human fingers (2D) and forearm (3D) using a LED-based system. Spatiotemporal SVD greatly enhanced the PA signals of blood vessels corrupted by noise while preserving a high temporal resolution to slow motions, improving the SNR of in vivo PA images by 1.1, 0.7, and 1.9 times compared to single frame-based wavelet denoising, averaging across 200 frames, and single frame without denoising, respectively. The proposed method demonstrated a processing time of around 50 \mus per frame with SVD acceleration and GPU. Thus, spatiotemporal SVD is well suited to PA imaging systems with low-energy excitation light sources for real-time in vivo applications.

eess.IV↗

arXiv2019

Estimating Spatially-Smoothed Fiber Orientation Distribution from Diffusion-MRI Experiments

Diffusion-weighted magnetic resonance imaging (D-MRI) is a noninvasive in vivo technique for probing the microstructural architecture of biological tissues. At each voxel, the fiber orientation distribution (FOD) characterizes local fiber configurations and orientations and is therefore a central object of estimation in D-MRI analysis. We propose the Nearest-Neighbor Adaptive Regression Model (NARM), a spatially adaptive framework for FOD estimation that performs weighted local likelihood estimation over nested spatial neighborhoods, where the weights jointly encode spatial proximity and similarity among neighboring FODs, measured by either the optimal transport or Hellinger distance. To prevent over-smoothing while preserving structural heterogeneity, we introduce a voxel-wise rescaling scheme and a data-driven stopping rule based on minimum nearest-neighbor dissimilarity. We further develop a configuration-aware strategy for selecting the similarity-smoothing parameter, allowing the smoothing strength to adapt to local fiber complexity. Simulation studies demonstrate that NARM improves FOD estimation accuracy relative to voxel-wise methods and the existing spatial smoothing approach PMARM. Application to test-retest data from the Human Connectome Project additionally shows that NARM yields more reproducible FOD estimates. Implementation details and scripts for the simulation and real data analyses are available at https://github.com/jie108/NARM

stat.AP↗