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Towards Portable Large-Scale Image Processing with High-Performance Computing.
Huo Y, Blaber J, Damon SM, Boyd BD, Bao S, Parvathaneni P, Noguera CB, Chaganti S, Nath V, Greer JM, Lyu I, French WR, Newton AT, Rogers BP, Landman BA
(2018) J Digit Imaging 31: 304-314
MeSH Terms: Diagnostic Imaging, Humans, Image Processing, Computer-Assisted, Information Storage and Retrieval, Radiology Information Systems
Show Abstract · Added March 18, 2020
High-throughput, large-scale medical image computing demands tight integration of high-performance computing (HPC) infrastructure for data storage, job distribution, and image processing. The Vanderbilt University Institute for Imaging Science (VUIIS) Center for Computational Imaging (CCI) has constructed a large-scale image storage and processing infrastructure that is composed of (1) a large-scale image database using the eXtensible Neuroimaging Archive Toolkit (XNAT), (2) a content-aware job scheduling platform using the Distributed Automation for XNAT pipeline automation tool (DAX), and (3) a wide variety of encapsulated image processing pipelines called "spiders." The VUIIS CCI medical image data storage and processing infrastructure have housed and processed nearly half-million medical image volumes with Vanderbilt Advanced Computing Center for Research and Education (ACCRE), which is the HPC facility at the Vanderbilt University. The initial deployment was natively deployed (i.e., direct installations on a bare-metal server) within the ACCRE hardware and software environments, which lead to issues of portability and sustainability. First, it could be laborious to deploy the entire VUIIS CCI medical image data storage and processing infrastructure to another HPC center with varying hardware infrastructure, library availability, and software permission policies. Second, the spiders were not developed in an isolated manner, which has led to software dependency issues during system upgrades or remote software installation. To address such issues, herein, we describe recent innovations using containerization techniques with XNAT/DAX which are used to isolate the VUIIS CCI medical image data storage and processing infrastructure from the underlying hardware and software environments. The newly presented XNAT/DAX solution has the following new features: (1) multi-level portability from system level to the application level, (2) flexible and dynamic software development and expansion, and (3) scalable spider deployment compatible with HPC clusters and local workstations.
0 Communities
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MeSH Terms
Evaluation of TSPO PET Ligands [F]VUIIS1009A and [F]VUIIS1009B: Tracers for Cancer Imaging.
Tang D, Li J, Buck JR, Tantawy MN, Xia Y, Harp JM, Nickels ML, Meiler J, Manning HC
(2017) Mol Imaging Biol 19: 578-588
MeSH Terms: Animals, Binding Sites, Blood Proteins, Carrier Proteins, Cell Line, Tumor, Diagnostic Imaging, Fluorine Radioisotopes, Glioma, Ligands, Male, Mice, Inbred C57BL, Positron-Emission Tomography, Rats, Tissue Distribution, Whole Body Imaging
Show Abstract · Added April 6, 2017
PURPOSE - Positron emission tomography (PET) ligands targeting translocator protein (TSPO) are potential imaging diagnostics of cancer. In this study, we report two novel, high-affinity TSPO PET ligands that are 5,7 regioisomers, [F]VUIIS1009A ([F]3A) and [F]VUIIS1009B ([F]3B), and their initial in vitro and in vivo evaluation in healthy mice and glioma-bearing rats.
PROCEDURES - VUIIS1009A/B was synthesized and confirmed by X-ray crystallography. Interactions between TSPO binding pocket and novel ligands were evaluated and compared with contemporary TSPO ligands using 2D H-N heteronuclear single quantum coherence (HSQC) spectroscopy. In vivo biodistribution of [F]VUIIS1009A and [F]VUIIS1009B was carried out in healthy mice with and without radioligand displacement. Dynamic PET imaging data were acquired simultaneously with [F]VUIIS1009A/B injections in glioma-bearing rats, with binding reversibility and specificity evaluated by radioligand displacement. In vivo radiometabolite analysis was performed using radio-TLC, and quantitative analysis of PET data was performed using metabolite-corrected arterial input functions. Imaging was validated with histology and immunohistochemistry.
RESULTS - Both VUIIS1009A (3A) and VUIIS1009B (3B) were found to exhibit exceptional binding affinity to TSPO, with observed IC values against PK11195 approximately 500-fold lower than DPA-714. However, HSQC NMR suggested that VUIIS1009A and VUIIS1009B share a common binding pocket within mammalian TSPO (mTSPO) as DPA-714 and to a lesser extent, PK11195. [F]VUIIS1009A ([F]3A) and [F]VUIIS1009B ([F]3B) exhibited similar biodistribution in healthy mice. In rats bearing C6 gliomas, both [F]VUIIS1009A and [F]VUIIS1009B exhibited greater binding potential (k /k )in tumor tissue compared to [F]DPA-714. Interestingly, [F]VUIIS1009B exhibited significantly greater tumor uptake (V ) than [F]VUIIS1009A, which was attributed primarily to greater plasma-to-tumor extraction efficiency.
CONCLUSIONS - The novel PET ligand [F]VUIIS1009B exhibits promising characteristics for imaging glioma; its superiority over [F]VUIIS1009A, a regioisomer, appears to be primarily due to improved plasma extraction efficiency. Continued evaluation of [F]VUIIS1009B as a high-affinity TSPO PET ligand for precision medicine appears warranted.
1 Communities
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15 MeSH Terms
Advances in imaging approaches to fracture risk evaluation.
Manhard MK, Nyman JS, Does MD
(2017) Transl Res 181: 1-14
MeSH Terms: Animals, Diagnostic Imaging, Fractures, Bone, Humans, Magnetic Resonance Imaging, Risk Assessment, Tomography, X-Ray Computed
Show Abstract · Added November 7, 2016
Fragility fractures are a growing problem worldwide, and current methods for diagnosing osteoporosis do not always identify individuals who require treatment to prevent a fracture and may misidentify those not a risk. Traditionally, fracture risk is assessed using dual-energy X-ray absorptiometry, which provides measurements of areal bone mineral density at sites prone to fracture. Recent advances in imaging show promise in adding new information that could improve the prediction of fracture risk in the clinic. As reviewed herein, advances in quantitative computed tomography (QCT) predict hip and vertebral body strength; high-resolution HR-peripheral QCT (HR-pQCT) and micromagnetic resonance imaging assess the microarchitecture of trabecular bone; quantitative ultrasound measures the modulus or tissue stiffness of cortical bone; and quantitative ultrashort echo-time MRI methods quantify the concentrations of bound water and pore water in cortical bone, which reflect a variety of mechanical properties of bone. Each of these technologies provides unique characteristics of bone and may improve fracture risk diagnoses and reduce prevalence of fractures by helping to guide treatment decisions.
Copyright © 2016 Elsevier Inc. All rights reserved.
2 Communities
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7 MeSH Terms
Investigation of Bias in Continuous Medical Image Label Fusion.
Xing F, Prince JL, Landman BA
(2016) PLoS One 11: e0155862
MeSH Terms: Algorithms, Diagnostic Imaging, Humans, Image Enhancement, Image Interpretation, Computer-Assisted, Pattern Recognition, Automated
Show Abstract · Added November 2, 2016
Image labeling is essential for analyzing morphometric features in medical imaging data. Labels can be obtained by either human interaction or automated segmentation algorithms, both of which suffer from errors. The Simultaneous Truth and Performance Level Estimation (STAPLE) algorithm for both discrete-valued and continuous-valued labels has been proposed to find the consensus fusion while simultaneously estimating rater performance. In this paper, we first show that the previously reported continuous STAPLE in which bias and variance are used to represent rater performance yields a maximum likelihood solution in which bias is indeterminate. We then analyze the major cause of the deficiency and evaluate two classes of auxiliary bias estimation processes, one that estimates the bias as part of the algorithm initialization and the other that uses a maximum a posteriori criterion with a priori probabilities on the rater bias. We compare the efficacy of six methods, three variants from each class, in simulations and through empirical human rater experiments. We comment on their properties, identify deficient methods, and propose effective methods as solution.
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6 MeSH Terms
Focus on Imaging Mass Spectrometry, Honoring Dr. Richard M. Caprioli, Recipient of the 2014 ASMS Award for a Distinguished Contribution in Mass Spectrometry.
Norris JL, Bierbaum VM
(2015) J Am Soc Mass Spectrom 26: 847-9
MeSH Terms: Animals, Awards and Prizes, Diagnostic Imaging, History, 20th Century, History, 21st Century, Humans, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, United States
Added April 10, 2018
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National Trends in Followup Imaging after Pyeloplasty in Children in the United States.
Hsi RS, Holt SK, Gore JL, Lendvay TS, Harper JD
(2015) J Urol 194: 777-82
MeSH Terms: Adolescent, Child, Child, Preschool, Diagnostic Imaging, Diagnostic Techniques, Urological, Female, Follow-Up Studies, Humans, Hydronephrosis, Infant, Kidney Pelvis, Male, Multicystic Dysplastic Kidney, Postoperative Care, United States, Ureteral Obstruction, Urologic Surgical Procedures
Show Abstract · Added January 16, 2018
PURPOSE - Radiographic followup after pyeloplasty for the correction of ureteropelvic junction obstruction is not well defined in children. We characterize trends in frequency and modality of postoperative imaging after open and minimally invasive pediatric pyeloplasty.
MATERIALS AND METHODS - Using the MarketScan® database, we identified patients 0 to 18 years old undergoing pyeloplasty between 2007 and 2013. Followup imaging was classified as functional (diuretic renography, excretory urography) or nonfunctional (ultrasound, computerized tomography, magnetic resonance imaging). We excluded patients with less than 24 months of postoperative enrollment in MarketScan. Multivariate logistic regression was performed to determine associations between demographic variables and imaging use patterns.
RESULTS - We identified 926 patients with a mean ± SD followup of 3.6 ± 1.3 years, of whom 30% underwent minimally invasive pyeloplasty. Overall 5.9% of patients had no postoperative imaging available. Within the first 6 months postoperatively 853 patients (91%) underwent at least 1 imaging study and 192 (24%) underwent renography. Within the first 12 months postoperatively 91% of patients underwent at least 1 imaging study, most commonly ultrasound. After 12 months almost a third of the patients were not followed with imaging. Of the 71% undergoing imaging most underwent ultrasound. Younger age and female gender were independently associated with frequent imaging (at least yearly) on multivariate logistic regression.
CONCLUSIONS - Following pediatric pyeloplasty there is variation in modality and frequency of imaging followup. The majority of patients are followed with renal ultrasound, with less frequent use of functional imaging. Almost a third of patients do not undergo followup imaging after 1 year.
Copyright © 2015 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.
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17 MeSH Terms
Histology-directed and imaging mass spectrometry: An emerging technology in ectopic calcification.
Taverna D, Boraldi F, De Santis G, Caprioli RM, Quaglino D
(2015) Bone 74: 83-94
MeSH Terms: Adolescent, Calcification, Physiologic, Calcinosis, Diagnostic Imaging, Female, Gene Ontology, Humans, Middle Aged, Phenotype, Principal Component Analysis, Protein Interaction Maps, Proteins, Pseudoxanthoma Elasticum, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
Show Abstract · Added February 12, 2015
The present study was designed to demonstrate the potential of an optimized histology directed protein identification combined with imaging mass spectrometry technology to reveal and identify molecules associated to ectopic calcification in human tissue. As a proof of concept, mineralized and non-mineralized areas were compared within the same dermal tissue obtained from a patient affected by Pseudoxanthoma elasticum, a genetic disorder characterized by calcification only at specific sites of soft connective tissues. Data have been technically validated on a contralateral dermal tissue from the same subject and compared with those from control healthy skin. Results demonstrate that this approach 1) significantly reduces the effects generated by techniques that, disrupting tissue organization, blend data from affected and unaffected areas; 2) demonstrates that, abolishing differences due to inter-individual variability, mineralized and non-mineralized areas within the same sample have a specific protein profile and have a different distribution of molecules; and 3) avoiding the bias of focusing on already known molecules, reveals a number of proteins that have been never related to the disease nor to the calcification process, thus paving the way for the selection of new molecules to be validated as pathogenic or as potential pharmacological targets.
Copyright © 2015. Published by Elsevier Inc.
1 Communities
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14 MeSH Terms
Cholinergic capacity mediates prefrontal engagement during challenges to attention: evidence from imaging genetics.
Berry AS, Blakely RD, Sarter M, Lustig C
(2015) Neuroimage 108: 386-95
MeSH Terms: Adult, Attention, Cholinergic Fibers, Diagnostic Imaging, Female, Humans, Magnetic Resonance Imaging, Male, Membrane Transport Proteins, Multivariate Analysis, Prefrontal Cortex, Receptors, Cholinergic, Symporters
Show Abstract · Added February 12, 2015
In rodent studies, elevated cholinergic neurotransmission in right prefrontal cortex (PFC) is essential for maintaining attentional performance, especially in challenging conditions. Apparently paralleling the rises in acetylcholine seen in rodent studies, fMRI studies in humans reveal right PFC activation at or near Brodmann's areas 9 (BA 9) increases in response to elevated attentional demand. In the present study, we leveraged human genetic variability in the cholinergic system to test the hypothesis that the cholinergic system contributes to the BA 9 response to attentional demand. Specifically, we scanned (BOLD fMRI) participants with a polymorphism of the choline transporter gene that is thought to limit choline transport capacity (Ile89Val variant of the choline transporter gene SLC5A7, rs1013940) and matched controls while they completed a task previously used to demonstrate demand-related increases in right PFC cholinergic transmission in rats and right PFC activation in humans. As hypothesized, we found that although controls showed the typical pattern of robust BA 9 responses to increased attentional demand, Ile89Val participants did not. Further, pattern analysis of activation within this region significantly predicted participant genotype. Additional exploratory pattern classification analyses suggested that Ile89Val participants differentially recruited orbitofrontal cortex and parahippocampal gyrus to maintain attentional performance to the level of controls. These results contribute to a growing body of translational research clarifying the role of cholinergic signaling in human attention and functional neural measures, and begin to outline the risk and resiliency factors associated with potentially suboptimal cholinergic function with implications for disorders characterized by cholinergic dysregulation.
Copyright © 2015 Elsevier Inc. All rights reserved.
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13 MeSH Terms
Inhalable curcumin: offering the potential for translation to imaging and treatment of Alzheimer's disease.
McClure R, Yanagisawa D, Stec D, Abdollahian D, Koktysh D, Xhillari D, Jaeger R, Stanwood G, Chekmenev E, Tooyama I, Gore JC, Pham W
(2015) J Alzheimers Dis 44: 283-95
MeSH Terms: Administration, Inhalation, Alzheimer Disease, Amyloid beta-Protein Precursor, Animals, Anti-Inflammatory Agents, Non-Steroidal, Brain, Curcumin, Diagnostic Imaging, Disease Models, Animal, Humans, Mice, Mice, Inbred C57BL, Mice, Transgenic, Mutation, Plaque, Amyloid, Presenilin-1, Tissue Distribution
Show Abstract · Added January 20, 2015
Curcumin is a promising compound that can be used as a theranostic agent to aid research in Alzheimer's disease. Beyond its ability to bind to amyloid plaques, the compound can also cross the blood-brain barrier. Presently, curcumin can be applied only to animal models, as the formulation needed for iv injection renders it unfit for human use. Here, we describe a novel technique to aerosolize a curcumin derivative, FMeC1, and facilitate its safe delivery to the brain. Aside from the translational applicability of this approach, a study in the 5XFAD mouse model suggested that inhalation exposure to an aerosolized FMeC1 modestly improved the distribution of the compound in the brain. Additionally, immunohistochemistry data confirms that following aerosol delivery, FMeC1 binds amyloid plaques expressed in the hippocampal areas and cortex.
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17 MeSH Terms
Fluorescence-based endoscopic imaging of Thomsen-Friedenreich antigen to improve early detection of colorectal cancer.
Sakuma S, Yu JY, Quang T, Hiwatari K, Kumagai H, Kao S, Holt A, Erskind J, McClure R, Siuta M, Kitamura T, Tobita E, Koike S, Wilson K, Richards-Kortum R, Liu E, Washington K, Omary R, Gore JC, Pham W
(2015) Int J Cancer 136: 1095-103
MeSH Terms: Adenocarcinoma, Animals, Antigens, Tumor-Associated, Carbohydrate, Biomarkers, Tumor, Colonoscopy, Colorectal Neoplasms, Diagnostic Imaging, Early Detection of Cancer, Female, Fluorescence, Fluorescent Dyes, Immunoenzyme Techniques, Mice, Mice, Inbred C57BL, Nanospheres, Rats, Rats, Nude, Tumor Cells, Cultured
Show Abstract · Added February 12, 2015
Thomsen-Friedenreich (TF) antigen belongs to the mucin-type tumor-associated carbohydrate antigen. Notably, TF antigen is overexpressed in colorectal cancer (CRC) but is rarely expressed in normal colonic tissue. Increased TF antigen expression is associated with tumor invasion and metastasis. In this study, we sought to validate a novel nanobeacon for imaging TF-associated CRC in a preclinical animal model. We developed and characterized the nanobeacon for use with fluorescence colonoscopy. In vivo imaging was performed on an orthotopic rat model of CRC. Both white light and fluorescence colonoscopy methods were utilized to establish the ratio-imaging index for the probe. The nanobeacon exhibited specificity for TF-associated cancer. Fluorescence colonoscopy using the probe can detect lesions at the stage which is not readily confirmed by conventional visualization methods. Further, the probe can report the dynamic change of TF expression as tumor regresses during chemotherapy. Data from this study suggests that fluorescence colonoscopy can improve early CRC detection. Supplemented by the established ratio-imaging index, the probe can be used not only for early detection, but also for reporting tumor response during chemotherapy. Furthermore, since the data obtained through in vivo imaging confirmed that the probe was not absorbed by the colonic mucosa, no registered toxicity is associated with this nanobeacon. Taken together, these data demonstrate the potential of this novel probe for imaging TF antigen as a biomarker for the early detection and prediction of the progression of CRC at the molecular level.
© 2014 UICC.
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18 MeSH Terms