scholarly journals PET Image Reconstruction with Kernel and Kernel Space Composite Regularizer

Author(s):  
Shiyao Guo ◽  
Yuxia Sheng ◽  
Shenpeng Li ◽  
Li Chai ◽  
Jingxin Zhang

<div>Represented by the kernelized expectation maximization (KEM), the kernelized maximum-likelihood (ML) expectation maximization (EM) methods have recently gained prominence in PET image reconstruction, outperforming many previous state-of-the-art methods. But they are not immune to the problems of non-kernelized MLEM methods in potentially large reconstruction variance and high sensitivity to iteration number. Also, it is generally difficult to simultaneously reduce image variance and preserve image details using kernels. To solve these problems, this paper presents a novel regularized KEM (RKEM) method with a kernel space composite regularizer for PET image reconstruction. The composite regularizer consists of a convex kernel space graph regularizer that smoothes the kernel coefficients, a non-convex kernel space energy regularizer that enhances the coefficients’ energy, and a composition constant that guarantees the convexity of composite regularizer. These kernel space regularizers are based on the theory of data manifold and graph regularization and can be constructed from different prior image data for simultaneous image variance reduction and image detail preservation. Using this kernel space composite regularizer and the technique of optimization transfer, a globally convergent iterative algorithm is derived for RKEM reconstruction. Tests and comparisons on the simulated and in vivo data are presented to validate and evaluate the proposed algorithm, and demonstrate its better performance and advantages over KEM and other conventional methods.</div>

2021 ◽  
Author(s):  
Shiyao Guo ◽  
Yuxia Sheng ◽  
Shenpeng Li ◽  
Li Chai ◽  
Jingxin Zhang

<div>Represented by the kernelized expectation maximization (KEM), the kernelized maximum-likelihood (ML) expectation maximization (EM) methods have recently gained prominence in PET image reconstruction, outperforming many previous state-of-the-art methods. But they are not immune to the problems of non-kernelized MLEM methods in potentially large reconstruction variance and high sensitivity to iteration number. Also, it is generally difficult to simultaneously reduce image variance and preserve image details using kernels. To solve these problems, this paper presents a novel regularized KEM (RKEM) method with a kernel space composite regularizer for PET image reconstruction. The composite regularizer consists of a convex kernel space graph regularizer that smoothes the kernel coefficients, a non-convex kernel space energy regularizer that enhances the coefficients’ energy, and a composition constant that guarantees the convexity of composite regularizer. These kernel space regularizers are based on the theory of data manifold and graph regularization and can be constructed from different prior image data for simultaneous image variance reduction and image detail preservation. Using this kernel space composite regularizer and the technique of optimization transfer, a globally convergent iterative algorithm is derived for RKEM reconstruction. Tests and comparisons on the simulated and in vivo data are presented to validate and evaluate the proposed algorithm, and demonstrate its better performance and advantages over KEM and other conventional methods.</div>


PLoS ONE ◽  
2021 ◽  
Vol 16 (12) ◽  
pp. e0260374
Author(s):  
Shiyao Guo ◽  
Yuxia Sheng ◽  
Li Chai ◽  
Jingxin Zhang

Low count PET (positron emission tomography) imaging is often desirable in clinical diagnosis and biomedical research, but its images are generally very noisy, due to the very weak signals in the sinograms used in image reconstruction. To address this issue, this paper presents a novel kernel graph filtering method for dynamic PET sinogram denoising. This method is derived from treating the dynamic sinograms as the signals on a graph, and learning the graph adaptively from the kernel principal components of the sinograms to construct a lowpass kernel graph spectrum filter. The kernel graph filter thus obtained is then used to filter the original sinogram time frames to obtain the denoised sinograms for PET image reconstruction. Extensive tests and comparisons on the simulated and real life in-vivo dynamic PET datasets show that the proposed method outperforms the existing methods in sinogram denoising and image enhancement of dynamic PET at all count levels, especially at low count, with a great potential in real life applications of dynamic PET imaging.


2005 ◽  
Vol 25 (1_suppl) ◽  
pp. S678-S678
Author(s):  
Yasuhiro Akazawa ◽  
Yasuhiro Katsura ◽  
Ryohei Matsuura ◽  
Piao Rishu ◽  
Ansar M D Ashik ◽  
...  

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Nian Liu ◽  
Xiao Chen ◽  
Xia Sun ◽  
Xiaolian Sun ◽  
Junpeng Shi

AbstractPersistent luminescence nanoparticles (PLNPs) are unique optical materials that emit afterglow luminescence after ceasing excitation. They exhibit unexpected advantages for in vivo optical imaging of tumors, such as autofluorescence-free, high sensitivity, high penetration depth, and multiple excitation sources (UV light, LED, NIR laser, X-ray, and radiopharmaceuticals). Besides, by incorporating other functional molecules, such as photosensitizers, photothermal agents, or therapeutic drugs, PLNPs are also widely used in persistent luminescence (PersL) imaging-guided tumor therapy. In this review, we first summarize the recent developments in the synthesis and surface functionalization of PLNPs, as well as their toxicity studies. We then discuss the in vivo PersL imaging and multimodal imaging from different excitation sources. Furthermore, we highlight PLNPs-based cancer theranostics applications, such as fluorescence-guided surgery, photothermal therapy, photodynamic therapy, drug/gene delivery and combined therapy. Finally, future prospects and challenges of PLNPs in the research of translational medicine are also discussed.


2021 ◽  
Author(s):  
Xiyu Ma ◽  
Chao Zhang ◽  
Do Young Kim ◽  
Yanyan Huang ◽  
Elizabeth Chatt ◽  
...  

Abstract Protein ubiquitylation profoundly expands proteome functionality and diversifies cellular signaling processes, with recent studies providing ample evidence for its importance to plant immunity. To gain a proteome-wide appreciation of ubiquitylome dynamics during immune recognition, we employed a two-step affinity enrichment protocol based on a 6His-tagged ubiquitin (Ub) variant coupled with high sensitivity mass spectrometry to identify Arabidopsis proteins rapidly ubiquitylated upon plant perception of the microbe-associated molecular pattern (MAMP) peptide flg22. The catalog from 2-week-old seedlings treated for 30 minutes with flg22 contained 690 conjugates, 64 Ub footprints, and all seven types of Ub linkages, and included previously uncharacterized conjugates of immune components. In vivo ubiquitylation assays confirmed modification of several candidates upon immune elicitation, and revealed distinct modification patterns and dynamics for key immune components, including poly- and monoubiquitylation, as well as induced or reduced levels of ubiquitylation. Gene ontology and network analyses of the collection also uncovered rapid modification of the Ub-proteasome system itself, suggesting a critical auto-regulatory loop necessary for an effective MAMP-triggered immune response and subsequent disease resistance. Included targets were UBIQUITIN-CONJUGATING ENZYME 13 (UBC13) and proteasome component REGULATORY PARTICLE NON-ATPASE SUBUNIT 8b (RPN8b), whose subsequent biochemical and genetic analyses implied negative roles in immune elicitation. Collectively, our proteomic analyses further strengthened the connection between ubiquitylation and flg22-based immune signaling, identified components and pathways regulating plant immunity, and increased the database of ubiquitylated substrates in plants.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Md Imam Uddin ◽  
Tyler C. Kilburn ◽  
Sara Z. Jamal ◽  
Craig L. Duvall ◽  
John S. Penn

AbstractDiabetic retinopathy, retinopathy of prematurity and retinal vein occlusion are potentially blinding conditions largely due to their respective neovascular components. The development of real-time in vivo molecular imaging methods, to assess levels of retinal neovascularization (NV), would greatly benefit patients afflicted with these conditions. mRNA hybridization techniques offer a potential method to image retinal NV. The success of these techniques hinges on the selection of a target mRNA whose tissue levels and spatial expression patterns correlate closely with disease burden. Using a model of oxygen-induced retinopathy (OIR), we previously observed dramatic increases in retinal endoglin that localized to neovascular structures (NV), directly correlating with levels of neovascular pathology. Based on these findings, we have investigated Endoglin mRNA as a potential marker for imaging retinal NV in OIR mice. Also of critical importance, is the application of innovative technologies capable of detecting mRNAs in living systems with high sensitivity and specificity. To detect and visualize endoglin mRNA in OIR mice, we have designed and synthesized a novel imaging probe composed of short-hairpin anti-sense (AS) endoglin RNA coupled to a fluorophore and black hole quencher (AS-Eng shRNA). This assembly allows highly sensitive fluorescence emission upon hybridization of the AS-Eng shRNA to cellular endoglin mRNA. The AS-Eng shRNA is further conjugated to a diacyl-lipid (AS-Eng shRNA–lipid referred to as probe). The lipid moiety binds to serum albumin facilitating enhanced systemic circulation of the probe. OIR mice received intraperitoneal injections of AS-Eng shRNA–lipid. Ex vivo imaging of their retinas revealed specific endoglin mRNA dependent fluorescence superimposed on neovascular structures. Room air mice receiving AS-Eng shRNA–lipid and OIR mice receiving a non-sense control probe showed little fluorescence activity. In addition, we found that cells in neovascular lesions labelled with endoglin mRNA dependent fluorescence, co-labelled with the macrophage/microglia-associated marker IBA1. Others have shown that cells expressing macrophage/microglia markers associate with retinal neovascular structures in proportion to disease burden. Hence we propose that our probe may be used to image and to estimate the levels of retinal neovascular disease in real-time in living systems.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ossama Mahmoud ◽  
Mahmoud El-Sakka ◽  
Barry G. H. Janssen

AbstractMicrovascular blood flow is crucial for tissue and organ function and is often severely affected by diseases. Therefore, investigating the microvasculature under different pathological circumstances is essential to understand the role of the microcirculation in health and sickness. Microvascular blood flow is generally investigated with Intravital Video Microscopy (IVM), and the captured images are stored on a computer for later off-line analysis. The analysis of these images is a manual and challenging process, evaluating experiments very time consuming and susceptible to human error. Since more advanced digital cameras are used in IVM, the experimental data volume will also increase significantly. This study presents a new two-step image processing algorithm that uses a trained Convolutional Neural Network (CNN) to functionally analyze IVM microscopic images without the need for manual analysis. While the first step uses a modified vessel segmentation algorithm to extract the location of vessel-like structures, the second step uses a 3D-CNN to assess whether the vessel-like structures have blood flowing in it or not. We demonstrate that our two-step algorithm can efficiently analyze IVM image data with high accuracy (83%). To our knowledge, this is the first application of machine learning for the functional analysis of microvascular blood flow in vivo.


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