Selection Of Acquisition Parameters Research Articles

Targeted retinal spectroscopy: Towards a localized assessment of biomarkers in the eye fundus

Aims/Purpose: The non‐invasive evaluation of biomarkers for the screening, diagnosis, and monitoring of ocular and neurological diseases is receiving increasing attention. Targeted retinal spectroscopy (TRS) enables simultaneous imaging and high‐quality spectral analysis from specific regions of the eye fundus. It offers valuable information on the structure, composition, and function of retinal tissues. This study demonstrates the capabilities of TRS and assesses its effectiveness in retinal oximetry.Methods: The Zilia Ocular TRS platform was developed and evaluated. First, a reference target and a model eye were used to demonstrate the targeted spectral analysis. Then, Monte Carlo simulations were used to identify crucial TRS parameters—such as spectral range, resolution, noise, and tissue scattering—for retinal oximetry. Simultaneous imaging of the eye fundus and diffuse reflectance spectra acquisitions were performed in two targeted regions of the eye fundus of eight healthy subjects to determine blood oxygen saturation (StO2).Results: Experiments performed with the reference target and model eye showed precise and distinct spectral signatures for each targeted region. Simulation results showed that highest StO2 accuracy was obtained with a spectral range between 530 nm and 585 nm, while a resolution below 4 nm compromised the accuracy. In addition, acquisition areas larger than blood vessels led to an underestimation of StO2, and a linear correlation was found between the additive noise level and the variability of StO2. In vivo oximetry measurements revealed significant differences in StO2 between the optic nerve head and the parafovea.Conclusions: TRS opens up new possibilities for disease screening, diagnosis and monitoring, including assessing oximetry in glaucoma, diabetic retinopathy, age‐related macular degeneration, etc. To account for confounding factors, careful selection of acquisition parameters is crucial, as emphasized in this study.

An information theory model for optimizing quantitative magnetic resonance imaging acquisitions

Acquisition parameter selection is currently performed empirically for many quantitative MRI (qMRI) acquisitions. Tuning parameters for different scan times, tissues, and resolutions requires some amount of trial and error. There is an opportunity to quantitatively optimize these acquisition parameters in order to minimize variability of quantitative maps and post-processing techniques such as synthetic image generation. The objective of this work is to introduce and evaluate a quantitative method for selecting parameters that minimize image variability. An information theory framework was developed for this purpose and applied to a 3D-quantification using an interleaved Look-Locker acquisition sequence with T2 preparation pulse (3D-QALAS) signal model for qMRI. In this framework, mutual information is used to measure the information gained by a measurement as a function of acquisition parameters, quantifying the information content of potential acquisitions and allowing informed parameter selection. The information theory framework was tested on artificial data generated from a representative mathematical phantom, measurements acquired on a qMRI multiparametric imaging standard phantom, and in vivo measurements in a human brain. The phantom measurements showed that higher mutual information calculated by the model correlated with smaller coefficient of variation in the reconstructed parametric maps, and in vivo measurements demonstrated that information-based calibration of acquisition parameters resulted in a decrease in parametric map variability consistent with model predictions.

Exploration of continuous-flow benchtop NMR acquisition parameters and considerations for reaction monitoring.

This study focused on fundamental data acquisition parameter selection for a benchtop nuclear magnetic resonance (NMR) system with continuous flow, applicable for reaction monitoring. The effect of flow rate on the mixing behaviors within a flow cell was observed, along with an exponential decay relationship between flow rate and the apparent spin-lattice relaxation time (T1*) of benzaldehyde. We also monitored sensitivity (as determined by signal-to-noise ratios; SNRs) under various flow rates, analyte concentrations, and temperatures of the analyte flask. Results suggest that a maximum SNR can be achieved with low to medium flow rates and higher analyte concentrations. This was consistent with data collected with parameters that promote either slow or fast data acquisition. We further consider the effect of these conditions on the analyte's residence time, T1*, and magnetic field inhomogeneity that is a product of continuous flow. Altogether, our results demonstrate how fundamental acquisition parameters can be manipulated to achieve optimal data acquisition in continuous-flow NMR systems.

Strategies for radiation exposure-sparing in fluoroscopically guided invasive cardiovascular procedures.

Minimizing radiation exposure during x-ray fluoroscopically guided procedures is critical to patients and to medical personnel. Tableside adjustment of x-ray image acquisition parameters can vary the fluoroscopic radiation exposure rate. To determine the impact of adjusting four tableside controllable image acquisition parameters on x-ray fluoroscopic radiation exposure rate. We made fluoroscopic exposures of a standard radiologic phantom to measure radiation exposure rates as kerma•area product per second of exposure and milligray per x-ray pulse under all possible combinations of detector zoom mode, collimated image field size, fluoroscopy dose mode, and fluoroscopy pulse frequency. Kerma•area product per second was linearly proportional to pulse frequency. Selecting larger detector zoom modes, smaller collimated image field sizes and low dose fluoroscopy mode each decreased exposure rate. We found a > 20-fold variation in dose rates over the range of acquisition parameter combinations. Selecting the most appropriate fluoroscopy acquisition parameters enables physician operators to adjust radiation exposure rates over a large range. Judicious selection of acquisition parameters can reduce patient and medical personnel radiation exposure by as much as 95% compared to "standard" fluoroscopy protocol settings.

RawTools: Rapid and Dynamic Interrogation of Orbitrap Data Files for Mass Spectrometer System Management.

Optimizing the quality of proteomics data collected from a mass spectrometer (MS) requires careful selection of acquisition parameters and proper assessment of instrument performance. Software tools capable of extracting a broad set of information from raw files, including meta, scan, quantification, and identification data, are needed to provide guidance for MS system management. In this work, direct extraction and utilization of these data is demonstrated using RawTools, a standalone tool for extracting meta and scan data directly from raw MS files generated on Thermo Orbitrap instruments. RawTools generates summarized and detailed plain text outputs after parsing individual raw files, including scan rates and durations, duty cycle characteristics, precursor and reporter ion quantification, and chromatography performance. RawTools also contains a diagnostic module that includes an optional "preview" database search for facilitating informed decision-making related to optimization of MS performance based on a variety of metrics. RawTools has been developed in C# and utilizes the Thermo RawFileReader library and thus can process raw MS files with high speed and high efficiency on all major operating systems (Windows, MacOS, Linux). To demonstrate the utility of RawTools, the extraction of meta and scan data from both individual and large collections of raw MS files was carried out to identify problematic characteristics of instrument performance. Taken together, the combined rich feature-set of RawTools with the capability for interrogation of MS and experiment performance makes this software a valuable tool for proteomics researchers.

Evaluation of the effect of image noise on CT perfusion measurements using digital perfusion phantoms.

To assess the influence of image noise on computed tomography (CT) perfusion studies, CT perfusion software algorithms were evaluated for susceptibility to image noise and results applied to clinical perfusion studies. Digital perfusion phantoms were generated using a published deconvolution model to create time-attenuation curves (TACs) for 16 different combinations of blood flow (BF; 30/60/90/120 ml/100 ml/min) and flow extraction product (FEP; 10/20/30/40 ml/100 ml/min) corresponding to values encountered in clinical studies. TACs were distorted with Gaussian noise at 50 different strengths to approximate image noise, performing 200 repetitions for each noise level. A total of 160,000 TACs were evaluated by measuring BF and FEP with CT perfusion software, comparing results for the maximum slope and Patlak models with those obtained with a deconvolution model. To translate results to clinical practice, data of 23 patients from a CT perfusion study were assessed for image noise, and the accuracy of reported CT perfusion measurements was estimated. Perfusion measurements depend on image noise as means and standard deviations of BF and FEP over repetitions increase with increasing image noise, especially for low BF and FEP values. BF measurements derived by deconvolution show larger standard deviations than those performed with the maximum slope model. Image noise in the evaluated CT perfusion study was 26.46 ± 3.52 HU, indicating possible overestimation of BF by up to 85% in a clinical setting. Measurements of perfusion parameters depend heavily upon the magnitude of image noise, which has to be taken into account during selection of acquisition parameters and interpretation of results, e.g., as a quantitative imaging biomarker. • CT perfusion results depend heavily upon the magnitude of image noise. • Different CT perfusion models react differently to the presence of image noise. • Blood flow may be overestimated by 85% in clinical CT perfusion studies.

Optimizing the target detectability of cone beam CT performed in image‐guided radiation therapy for patients of different body sizes

PurposeThe target detectability of cone beam computed tomography (CBCT) performed in image‐guided radiation therapy (IGRT) was investigated to achieve sufficient image quality for patient positioning over a course of treatment session while maintaining radiation exposure from CBCT imaging as low as reasonably achievable (ALARA).MethodsBody CBCT scans operated in half‐fan mode were acquired with three different protocols: CBCTlowD, CBCTmidD, and CBCThighD, which resulted in weighted CT dose index (CTDIw) of 0.36, 1.43, and 2.78 cGy, respectively. An electron density phantom that is 18 cm in diameter was covered by four layers of 2.5‐cm‐thick bolus to simulate patients of different body sizes. Multivariate analysis was used to examine the impact of body size, radiation exposure, and tissue type on the target detectability of CBCT imaging, quantified as contrast‐to‐noise ratio (CNR).ResultsCBCTmidD allows sufficient target detection of adipose, breast, muscle, liver in a background of water for normal‐weight adults with cross‐sectional diameter less than 28 cm, while CBCThighD is suitable for adult patients with larger body sizes or body mass index over 25 kg/m2. Once the cross‐sectional diameter of adult patients is larger than 35 cm, the CTDIw of CBCT scans should be higher than 2.78 cGy to achieve required CNR. As for pediatric and adolescent patients with cross‐sectional diameter less than 25 cm, CBCTlowD is able to produce images with sufficient target detection.ConclusionThe target detectability of soft tissues in default CBCT scans may not be sufficient for overweight or obese adults. Contrary, pediatric and adolescent patients would receive unnecessarily high radiation exposure from default CBCT scans. Therefore, the selection of acquisition parameters for CBCT scans optimized according to patient body size was proposed to ensure sufficient image quality for daily patient positioning in radiation therapy while achieving the ALARA principle.

Fundamental limits of image registration performance: Effects of image noise and resolution in CT-guided interventions.

In image-guided procedures, image acquisition is often performed primarily for the task of geometrically registering information from another image dataset, rather than detection / visualization of a particular feature. While the ability to detect a particular feature in an image has been studied extensively with respect to image quality characteristics (noise, resolution) and is an ongoing, active area of research, comparatively little has been accomplished to relate such image quality characteristics to registration performance. To establish such a framework, we derived Cramer-Rao lower bounds (CRLB) for registration accuracy, revealing the underlying dependencies on image variance and gradient strength. The CRLB was analyzed as a function of image quality factors (in particular, dose) for various similarity metrics and compared to registration accuracy using CT images of an anthropomorphic head phantom at various simulated dose levels. Performance was evaluated in terms of root mean square error (RMSE) of the registration parameters. Analysis of the CRLB shows two primary dependencies: 1) noise variance (related to dose); and 2) sum of squared image gradients (related to spatial resolution and image content). Comparison of the measured RMSE to the CRLB showed that the best registration method, RMSE achieved the CRLB to within an efficiency factor of 0.21, and optimal estimators followed the predicted inverse proportionality between registration performance and radiation dose. Analysis of the CRLB for image registration is an important step toward understanding and evaluating an intraoperative imaging system with respect to a registration task. While the CRLB is optimistic in absolute performance, it reveals a basis for relating the performance of registration estimators as a function of noise content and may be used to guide acquisition parameter selection (e.g., dose) for purposes of intraoperative registration.

Temporal artifact minimization in sonoelastography through optimal selection of imaging parameters.

Sonoelastography is an ultrasonic technique that uses Kasai's autocorrelation algorithms to generate qualitative images of tissue elasticity using external mechanical vibrations. In the absence of synchronization between the mechanical vibration device and the ultrasound system, the random initial phase and finite ensemble length of the data packets result in temporal artifacts in the sonoelastography frames and, consequently, in degraded image quality. In this work, the analytic derivation of an optimal selection of acquisition parameters (i.e., pulse repetition frequency, vibration frequency, and ensemble length) is developed in order to minimize these artifacts, thereby eliminating the need for complex device synchronization. The proposed rule was verified through experiments with heterogeneous phantoms, where the use of optimally selected parameters increased the average contrast-to-noise ratio (CNR) by more than 200% and reduced the CNR standard deviation by 400% when compared to the use of arbitrarily selected imaging parameters. Therefore, the results suggest that the rule for specific selection of acquisition parameters becomes an important tool for producing high quality sonoelastography images.

Effects of data acquisition parameters on the quality of sonoelastographic imaging.

Sonoelastography is an ultrasonic technique that provides qualitative and quantitative images of tissue elasticity. Even though the Kasai variance estimator is a key part of the sonoelastographic image formation, there are no studies that demonstrate that its performance using discrete time signals and finite sized ensemble lengths is optimal. In this work, the influence of the selection of acquisition parameters (pulse repetition frequency or PRF, vibration frequency, and ensemble length) on the quality of the elastograms is studied. Simulations are carried out to define the optimal PRF and ensemble length given a vibration frequency in order to avoid artifacts which can severely degrade image quality. This empirical criterion is supported by sonoelastography experiments performed using two commercial scanners, where the variability increased from 4% to 42% at the worst selection of acquisition parameters. Although a further mathematical proof of the empirical findings is required, these results suggest that careful selection of PRF, vibration frequency and ensemble lengths is required to ensure unbiased sonoelastograms.

Cerebrovascular MRI: a review of state-of-the-art approaches, methods and techniques.

Cerebrovascular imaging is of great interest in the understanding of neurological disease. MRI is a non-invasive technology that can visualize and provide information on: (i) the structure of major blood vessels; (ii) the blood flow velocity in these vessels; and (iii) the microcirculation, including the assessment of brain perfusion. Although other medical imaging modalities can also interrogate the cerebrovascular system, MR provides a comprehensive assessment, as it can acquire many different structural and functional image contrasts whilst maintaining a high level of patient comfort and acceptance. The extent of examination is limited only by the practicalities of patient tolerance or clinical scheduling limitations. Currently, MRI methods can provide a range of metrics related to the cerebral vasculature, including: (i) major vessel anatomy via time-of-flight and contrast-enhanced imaging; (ii) blood flow velocity via phase contrast imaging; (iii) major vessel anatomy and tissue perfusion via arterial spin labeling and dynamic bolus passage approaches; and (iv) venography via susceptibility-based imaging. When designing an MRI protocol for patients with suspected cerebral vascular abnormalities, it is appropriate to have a complete understanding of when to use each of the available techniques in the 'MR angiography toolkit'. In this review article, we: (i) overview the relevant anatomy, common pathologies and alternative imaging modalities; (ii) describe the physical principles and implementations of the above listed methods; (iii) provide guidance on the selection of acquisition parameters; and (iv) describe the existing and potential applications of MRI to the cerebral vasculature and diseases. The focus of this review is on obtaining an understanding through the application of advanced MRI methodology of both normal and abnormal blood flow in the cerebrovascular arteries, capillaries and veins.

Anthropomorphic chest phantom imaging – The potential for dose creep in computed radiography

For film-based radiography the operator had to be exact in the selection of acquisition parameters or the image could easily become under- or over-exposed. By contrast, digital technology allows for a much greater tolerance of acquisition factor selection which would still give an image of acceptable diagnostic quality. In turn this greater tolerance allows for the operator to increase effective dose for little or no penalty in image quality. The purpose of this article is to determine how image quality and lesion visibility vary with effective dose (E) in order to identify how much overexposure could be tolerated within the radiograph. Using an anthropomorphic chest phantom with ground glass lesions we determined how perceptual image quality and E varied over a wide range of acquisition conditions. Perceptual image quality comprised of image quality and lesion visibility. E was calculated using Monte Carlo method; image quality was determined using a two alternative forced choice (2AFC) method and the quality criteria were partly informed from European guidelines. Five clinicians with significant experience in image reading scored the images for quality (intraclass correlation coefficient 0.869). Image quality and lesion visibility had a close correlation (R2 > 0.8). The tolerance for over-exposure, whilst still acquiring an image of acceptable quality, increases with decreasing kV and increasing source to image distance (SID). The maximum over-exposure factor (ratio of maximum E to minimum E that produce images of acceptable quality) possible was 139 (at 125 cm and 60 kV). Given the phantom had characteristics similar to the human thorax we propose that that potential for overexposure in a human whilst still obtaining an image of acceptable perceptual image quality is very high. Further research into overexposure tolerance and dose creep should be undertaken.

Off-resonance frequency filtered magnetic resonance imaging

One of the main problems with rapid magnetic resonance imaging (MRI) techniques is the artifacts that result from off-resonance effects. The proposed off-resonance frequency filtered MRI (OFF-MRI) method focuses on the elimination of off-resonance components from the image of the observed object. To maintain imaging speed and simultaneously achieve good frequency selectivity, MRI is divided into two steps: signal acquisition and post-processing. After the preliminary phase in which we determine imaging parameters, MRI takes place; the signal from the same object is successively acquired M times. As a result, we obtain M partial signals in k-space, from which we form the image of the observed object in the post-processing phase, after signal acquisition has been completed. This paper demonstrates that with proper selection of acquisition parameters and weighting coefficients in the post-processing phase, OFF-MRI is equivalent to filtering the signal by finite impulse response filter of length M. It is shown that with M successive acquisitions M-1 off-resonance components can be eliminated (filtered-out) from images, and therefore, only two acquisitions are needed to eliminate one off-resonance components. On the other hand, with OFF-MRI, it is also possible to form the image of an arbitrary off-resonance component by eliminating all other off-resonance components, including the on-resonance component. The proposed OFF-MRI method is suitable for MRI where rapid acquisition is required and elimination of off-resonance components can improve reliability of measurements.

Multicomponent T2 relaxation analysis in cartilage

MR techniques are sensitive to the early stages of osteoarthritis, characterized by disruption of collagen and loss of proteoglycan (PG), but are of limited specificity. Here, water compartments in normal and trypsin-degraded bovine nasal cartilage were identified using a nonnegative least squares multiexponential analysis of T(2) relaxation. Three components were detected: T(2,1)=2.3 ms, T(2,2)=25.2 ms, and T(2,3)=96.3 ms, with fractions w(1)=6.2%, w(2)=14.5%, and w(3)=79.3%, respectively. Trypsinization resulted in increased (P<0.01) values of T(2,2)=64.2 ms and T(2,3)=149.4 ms, supporting their assignment to water compartments that are bound and loosely associated with PG, respectively. The T(2) of the rapidly relaxing component was not altered by digestion, supporting assignment to relatively immobile collagen-bound water. Relaxation data were simulated for a range of TE, number of echoes, and SNR to guide selection of acquisition parameters and assess the accuracy and precision of experimental results. Based on this, the expected experimental accuracy of measured T(2)s and associated weights was within 2% and 4% respectively, with precision within 1% and 3%. These results demonstrate the potential of multiexponential T(2) analysis to increase the specificity of MR characterization of cartilage.

MDCT of renal and mesenteric vessels.

Computed tomography angiography (CTA) with multiple detector-row CT (MDCT) has evolved into an established technique for non-invasive imaging of renal and mesenteric vessels. With adequate selection of acquisition parameters (thin collimation) high spatial-resolution volumetric data sets for subsequent 2D and 3D reformation can be acquired. Contrast medium (CM) injection parameters need to be adjusted to the acquisition speed of the scanners. Whereas fast acquisitions allow a reduction of total CM volume in the setting of CTA, this is not the case when CTA is combined with a second-phase abdominal MDCT acquisition for parenchymal (e.g., hepatic) imaging. Renal CTA is an accurate and reliable test for visualizing vascular anatomy and renal artery stenosis, and therefore a viable alternative to MRA in the assessment of patients with renovascular hypertension and in potential living related renal donors. CTA, combined with abdominal/parenchymal MDCT is a first-line diagnostic test in patients with suspected abdominal vascular emergencies, such as acute mesenteric ischemia, and an excellent tool to assess a wide variety of vascular abnormalities of the abdominal viscera.

Determination of Residual Oil Saturation by Use of Enhanced Diffusion

Summary The enhanced diffusion method (EDM) exploits the diffusion contrast between oil and water separating their respective nuclear magnetic resonance (NMR) signals. Unlike standard NMR logs acquired with short interecho time (TE), measurements, EDM data are acquired using long TE accentuating diffusion. Fundamentally the EDM establishes an absolute upper bound for the T2 of water, thus any T2's greater than this limit unambiguously indicates that oil is present. The EDM's best application is with intermediate viscosity oils (approximately 1 to 50 cp) complementing other NMR hydrocarbon-typing applications designed for lighter hydrocarbons (i.e., the differential spectrum method). While expanding the viscosity range of NMR hydrocarbon-typing applications, the EDM also provides a method by which to determine residual oil saturation (ROS), which is the main focus of this article. The potential use of NMR as a direct indicator of hydrocarbon saturation via techniques such as the differential spectrum method (DSM) has generated significant interest in the petrophysical community in recent years. Although originally developed for applications involving natural gas, the DSM has also been used successfully in light hydrocarbon environments. However, success has been limited to the low end of the viscosity spectrum because of the T1 separation requirements between the brine and hydrocarbon phases. The T1 separation requirement imposed on diffusion applications in higher viscosity oils can be eliminated by using the EDM, where diffusion is turned into the dominant relaxation mode for the wetting brine phase. Given that brine is more diffusive than the hydrocarbons, the longest apparent T2 from the brine phase can be made short enough to cause separation between the two phases in T2 space, thereby eliminating the need for T1 separation. Wait time manipulation can then be used to quantify hydrocarbon volumes when the two phases are separated in the T2 domain. In this article we focus on determination of the residual oil saturation using the EDM, while also providing guidelines for job screening and acquisition parameter selection. Several case histories that are provided are used to illustrate the basic concepts and different methodologies available.

Sensitivity Optimization in Continuous-Flow FTNMR

Equations simulating the steady-state magnetization of liquids in continuous-flow FTNMR are derived using a classical vector model, assuming plug flow. These equations are applied to calculation of (S/N)t, the relative signal/noise per unit time of any nucleus undergoing any degree of Overhauser enhancement either in the detection cell or upstream, or both, and to optimization of experimental conditions, including pulse repetition timeTrep, pulse angle β, and flow rate. Ideal parameters include a pulse angle of 90° and aTrepvalue equal to sample residence time in the NMR detection cell. Optimal flow rates are directly proportional to the premagnetization volume (the portion of sample equilibrated with the magnetic field prior to detection) and inversely proportional to spin–lattice relaxation timesT1. Optimal premagnetization times are smaller than previously assumed, varying from about 1.1 to 1.9T1values. (S/N)tfor static FTNMR is discussed in some detail, and a new graphical method is presented for its optimization. Flow advantage, the (S/N)tof optimized flow FTNMR experiments compared to that of static FTNMR in a given detection cell, is proportional to the square root of the ratio of premagnetization to detection cell volumes, and virtually independent of[formula]where[formula]is the apparent transverse-relaxation time. The theory is applied to examples from recent literature, including dynamic electron–nuclear polarization, and the literature is critically reviewed. The analysis shows that claims by previous authors of recycled flow FTNMR by itself leading to increased (S/N)tfor slowly relaxing resonances are misleading, owing to underdetermination of (S/N)tin static measurements and failure to account for greater sample sizes required in flow experiments. For monitoring and control of chemical processes, the theory presented here enables the first rational basis for the design of a flow FTNMR apparatus and for the selection of acquisition parameters.