Comparing Deep Learning Frameworks for Photoacoustic Tomography Image Reconstruction.
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ABSTRACT:
SUBMITTER: Hsu KT
PROVIDER: S-EPMC8165448 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Conventional reconstruction algorithms (e.g., delay-and-sum) used in photoacoustic imaging (PAI) provide a fast solution while many artifacts remain, especially for limited-view with ill-posed problem. In this paper, we propose a new convolutional neural network (CNN) framework Y-Net: a CNN architecture to reconstruct the initial PA pressure distribution by optimizing both raw data and beamformed images once. The network combines two encoders with one decoder path, which optimally utilizes more information from raw data and beamformed image. We compared our result with some ablation studies, and the results of the test set show better performance compared with conventional reconstruction algorithms and other deep learning method (U-Net). Both in-vitro and in-vivo experiments are used to validated our method, which still performs better than other existing methods. The proposed Y-Net architecture also has high potential in medical image reconstruction for other imaging modalities beyond PAI.
| S-EPMC7322183 | biostudies-literature
Project description:ObjectivesDeep-learning image reconstruction (DLIR) offers unique opportunities for reducing image noise without degrading image quality or diagnostic accuracy in coronary CT angiography (CCTA). The present study aimed at exploiting the capabilities of DLIR to reduce radiation dose and assess its impact on stenosis severity, plaque composition analysis, and plaque volume quantification.MethodsThis prospective study includes 50 patients who underwent two sequential CCTA scans at normal-dose (ND) and lower-dose (LD). ND scans were reconstructed with Adaptive Statistical Iterative Reconstruction-Veo (ASiR-V) 100%, and LD scans with DLIR. Image noise (in Hounsfield units, HU) and quantitative plaque volumes (in mm3) were assessed quantitatively. Stenosis severity was visually categorized into no stenosis (0%), stenosis (< 20%, 20-50%, 51-70%, 71-90%, 91-99%), and occlusion (100%). Plaque composition was classified as calcified, non-calcified, or mixed.ResultsReduction of radiation dose from ND scans with ASiR-V 100% to LD scans with DLIR at the highest level (DLIR-H; 1.4 mSv vs. 0.8 mSv, p < 0.001) had no impact on image noise (28 vs. 27 HU, p = 0.598). Reliability of stenosis severity and plaque composition was excellent between ND scans with ASiR-V 100% and LD scans with DLIR-H (intraclass correlation coefficients of 0.995 and 0.974, respectively). Comparison of plaque volumes using Bland-Altman analysis revealed a mean difference of - 0.8 mm3 (± 2.5 mm3) and limits of agreement between - 5.8 and + 4.1 mm3.ConclusionDLIR enables a reduction in radiation dose from CCTA by 43% without significant impact on image noise, stenosis severity, plaque composition, and quantitative plaque volume.Key points•Deep-learning image reconstruction (DLIR) enables radiation dose reduction by over 40% for coronary computed tomography angiography (CCTA). •Image noise remains unchanged between a normal-dose CCTA reconstructed by ASiR-V and a lower-dose CCTA reconstructed by DLIR. •There is no impact on the assessment of stenosis severity, plaque composition, and quantitative plaque volume between the two scans.
| S-EPMC8921160 | biostudies-literature
Project description:Photoacoustic tomography (PAT) images contain inherent distortions due to the imaging system and heterogeneous tissue properties. Improving image quality requires the removal of these system distortions. While model-based approaches and data-driven techniques have been proposed for PAT image restoration, achieving accurate and robust image recovery remains challenging. Recently, deep-learning-based image deconvolution approaches have shown promise for image recovery. However, PAT imaging presents unique challenges, including spatially varying resolution and the absence of ground truth data. Consequently, there is a pressing need for a novel learning strategy specifically tailored for PAT imaging. Herein, we propose a configurable network model named Deep hybrid Image-PSF Prior (DIPP) that builds upon the physical image degradation model of PAT. DIPP is an unsupervised and deeply learned network model that aims to extract the ideal PAT image from complex system degradation. Our DIPP framework captures the degraded information solely from the acquired PAT image, without relying on ground truth or labeled data for network training. Additionally, we can incorporate the experimentally measured Point Spread Functions (PSFs) of the specific PAT system as a reference to further enhance performance. To evaluate the algorithm's effectiveness in addressing multiple degradations in PAT, we conduct extensive experiments using simulation images, publicly available datasets, phantom images, and in vivo small animal imaging data. Comparative analyses with classical analytical methods and state-of-the-art deep learning models demonstrate that our DIPP approach achieves significantly improved restoration results in terms of image details and contrast.
| S-EPMC10413197 | biostudies-literature
Project description:Cryogenic electron tomography (cryoET) allows visualization of cellular structures in situ. However, anisotropic resolution arising from the intrinsic "missing-wedge" problem has presented major challenges in visualization and interpretation of tomograms. Here, we have developed IsoNet, a deep learning-based software package that iteratively reconstructs the missing-wedge information and increases signal-to-noise ratio, using the knowledge learned from raw tomograms. Without the need for sub-tomogram averaging, IsoNet generates tomograms with significantly reduced resolution anisotropy. Applications of IsoNet to three representative types of cryoET data demonstrate greatly improved structural interpretability: resolving lattice defects in immature HIV particles, establishing architecture of the paraflagellar rod in Eukaryotic flagella, and identifying heptagon-containing clathrin cages inside a neuronal synapse of cultured cells. Therefore, by overcoming two fundamental limitations of cryoET, IsoNet enables functional interpretation of cellular tomograms without sub-tomogram averaging. Its application to high-resolution cellular tomograms should also help identify differently oriented complexes of the same kind for sub-tomogram averaging.
| S-EPMC9617606 | biostudies-literature
Project description:Photoacoustic tomography (PAT) is a non-ionizing imaging modality capable of acquiring high contrast and resolution images of optical absorption at depths greater than traditional optical imaging techniques. Practical considerations with instrumentation and geometry limit the number of available acoustic sensors and their "view" of the imaging target, which result in image reconstruction artifacts degrading image quality. Iterative reconstruction methods can be used to reduce artifacts but are computationally expensive. In this work, we propose a novel deep learning approach termed pixel-wise deep learning (Pixel-DL) that first employs pixel-wise interpolation governed by the physics of photoacoustic wave propagation and then uses a convolution neural network to reconstruct an image. Simulated photoacoustic data from synthetic, mouse-brain, lung, and fundus vasculature phantoms were used for training and testing. Results demonstrated that Pixel-DL achieved comparable or better performance to iterative methods and consistently outperformed other CNN-based approaches for correcting artifacts. Pixel-DL is a computationally efficient approach that enables for real-time PAT rendering and improved image reconstruction quality for limited-view and sparse PAT.
| S-EPMC7244747 | biostudies-literature
Project description:Photoacoustic tomography (PAT) is a propitious imaging modality, which is helpful for biomedical study. However, fast PAT imaging and denoising is an exigent task in medical research. To address the problem, recently, methods based on compressed sensing (CS) have been proposed, which accede the low computational cost and high resolution for implementing PAT. Nevertheless, the imaging results of the sparsity-based methods strictly rely on sparsity and incoherence conditions. Furthermore, it is onerous to ensure that the experimentally acquired photoacoustic data meets CS's prerequisite conditions. In this work, a deep learning-based PAT (Deep-PAT)method is instigated to overcome these limitations. By using a neural network, Deep-PAT is not only able to reconstruct PAT from a fewer number of measurements without considering the prerequisite conditions of CS, but also can eliminate undersampled artifacts effectively. The experimental results demonstrate that Deep-PAT is proficient at recovering high-quality photoacoustic images using just 5% of the original measurement data. Besides this, compared with the sparsity-based method, it can be seen through statistical analysis that the quality is significantly improved by 30% (approximately), having average SSIM = 0.974 and PSNR = 29.88 dB with standard deviation ±0.007 and ±0.089, respectively, by the proposed Deep-PAT method. Also, a comparsion of multiple neural networks provides insights into choosing the best one for further study and practical implementation.
| S-EPMC7943731 | biostudies-literature
Project description:We investigated the effect of deep learning-based image reconstruction (DLIR) compared to iterative reconstruction on image quality in CT pulmonary angiography (CTPA) for suspected pulmonary embolism (PE). For 220 patients with suspected PE, CTPA studies were reconstructed using filtered back projection (FBP), adaptive statistical iterative reconstruction (ASiR-V 30%, 60% and 90%) and DLIR (low, medium and high strength). Contrast-to-noise ratio (CNR) served as the primary parameter of objective image quality. Subgroup analyses were performed for normal weight, overweight and obese individuals. For patients with confirmed PE (n = 40), we further measured PE-specific CNR. Subjective image quality was assessed independently by two experienced radiologists. CNR was lowest for FBP and enhanced with increasing levels of ASiR-V and, even more with increasing strength of DLIR. High strength DLIR resulted in an additional improvement in CNR by 29-67% compared to ASiR-V 90% (p < 0.05). PE-specific CNR increased by 75% compared to ASiR-V 90% (p < 0.05). Subjective image quality was significantly higher for medium and high strength DLIR compared to all other image reconstructions (p < 0.05). In CT pulmonary angiography, DLIR significantly outperforms iterative reconstruction for increasing objective and subjective image quality. This may allow for further reductions in radiation exposure in suspected PE.
| S-EPMC10827738 | biostudies-literature
Project description:SignificanceDynamic photoacoustic computed tomography (PACT) is a valuable imaging technique for monitoring physiological processes. However, current dynamic PACT imaging techniques are often limited to two-dimensional spatial imaging. Although volumetric PACT imagers are commercially available, these systems typically employ a rotating measurement gantry in which the tomographic data are sequentially acquired as opposed to being acquired simultaneously at all views. Because the dynamic object varies during the data-acquisition process, the sequential data-acquisition process poses substantial challenges to image reconstruction associated with data incompleteness. The proposed image reconstruction method is highly significant in that it will address these challenges and enable volumetric dynamic PACT imaging with existing preclinical imagers.AimThe aim of this study is to develop a spatiotemporal image reconstruction (STIR) method for dynamic PACT that can be applied to commercially available volumetric PACT imagers that employ a sequential scanning strategy. The proposed reconstruction method aims to overcome the challenges caused by the limited number of tomographic measurements acquired per frame.ApproachA low-rank matrix estimation-based STIR (LRME-STIR) method is proposed to enable dynamic volumetric PACT. The LRME-STIR method leverages the spatiotemporal redundancies in the dynamic object to accurately reconstruct a four-dimensional (4D) spatiotemporal image.ResultsThe conducted numerical studies substantiate the LRME-STIR method's efficacy in reconstructing 4D dynamic images from tomographic measurements acquired with a rotating measurement gantry. The experimental study demonstrates the method's ability to faithfully recover the flow of a contrast agent with a frame rate of 10 frames per second, even when only a single tomographic measurement per frame is available.ConclusionsThe proposed LRME-STIR method offers a promising solution to the challenges faced by enabling 4D dynamic imaging using commercially available volumetric PACT imagers. By enabling accurate STIRs, this method has the potential to significantly advance preclinical research and facilitate the monitoring of critical physiological biomarkers.
| S-EPMC10798269 | biostudies-literature
Project description:An intelligent sensing framework using Machine Learning (ML) and Deep Learning (DL) architectures to precisely quantify dielectrophoretic force invoked on microparticles in a textile electrode-based DEP sensing device is reported. The prediction accuracy and generalization ability of the framework was validated using experimental results. Images of pearl chain alignment at varying input voltages were used to build deep regression models using modified ML and CNN architectures that can correlate pearl chain alignment patterns of Saccharomyces cerevisiae(yeast) cells and polystyrene microbeads to DEP force. Various ML models such as K-Nearest Neighbor, Support Vector Machine, Random Forest, Neural Networks, and Linear Regression along with DL models such as Convolutional Neural Network (CNN) architectures of AlexNet, ResNet-50, MobileNetV2, and GoogLeNet have been analyzed in order to build an effective regression framework to estimate the force induced on yeast cells and microbeads. The efficiencies of the models were evaluated using Mean Absolute Error, Mean Absolute Relative, Mean Squared Error, R-squared, and Root Mean Square Error (RMSE) as evaluation metrics. ResNet-50 with RMSPROP gave the best performance, with a validation RMSE of 0.0918 on yeast cells while AlexNet with ADAM optimizer gave the best performance, with a validation RMSE of 0.1745 on microbeads. This provides a baseline for further studies in the application of deep learning in DEP aided Lab-on-Chip devices.
| S-EPMC9279499 | biostudies-literature
Project description:Recent advancements in deep learning for automated image processing and classification have accelerated many new applications for medical image analysis. However, most deep learning algorithms have been developed using reconstructed, human-interpretable medical images. While image reconstruction from raw sensor data is required for the creation of medical images, the reconstruction process only uses a partial representation of all the data acquired. Here, we report the development of a system to directly process raw computed tomography (CT) data in sinogram-space, bypassing the intermediary step of image reconstruction. Two classification tasks were evaluated for their feasibility of sinogram-space machine learning: body region identification and intracranial hemorrhage (ICH) detection. Our proposed SinoNet, a convolutional neural network optimized for interpreting sinograms, performed favorably compared to conventional reconstructed image-space-based systems for both tasks, regardless of scanning geometries in terms of projections or detectors. Further, SinoNet performed significantly better when using sparsely sampled sinograms than conventional networks operating in image-space. As a result, sinogram-space algorithms could be used in field settings for triage (presence of ICH), especially where low radiation dose is desired. These findings also demonstrate another strength of deep learning where it can analyze and interpret sinograms that are virtually impossible for human experts.
| S-EPMC6820559 | biostudies-literature