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Ideal versus human observer for long-tailed point spread functions: does deconvolution help?

The ideal observer represents a Bayesian approach to performing detection tasks. Since such tasks are frequently used as a prototype tasks for radiological imaging systems, the detectability measured at the output of an ideal detector can be used as a figure of merit to characterize the imaging system. For the detectability achieved by the ideal observer to be a good figure of merit, it should predict the ability of the human observer to perform the same detection task. Of great general interest, especially to the medical community, are imaging devices with long-tailed point spread functions (PSFs). Such PSFs may occur due to septal penetration in collimators, veiling glare in image intensifiers or scattered radiation in the body. We have investigated the effect that this type of PSF has on human visual signal detection and whether any improvement in performance can be gained by deconvolving the tails of the PSF. For the ideal observer, it is straightforward to show that the performance is independent of any linear, invertible deconvolution filter. Our psychophysical studies show, however, that performance of the human observer is indeed improved by deconvolution. The ideal observer is, therefore, not a good predictor of human observer performance for detection of a signal imaged through a long-tailed PSF. We offer some explanations for this discrepancy by using some characteristics of the visual process and suggest a standard of comparison for the human observer that takes into account these characteristics. A look at the performance of the non-prewhitening (npw) ideal observer, before and after deconvolution, also brings some good insight into this study.

Bayes Theorem

Enhancing and accelerating cell type deconvolution of large-scale spatial transcriptomics slices with dual network model.

MOTIVATION: Cell type deconvolution deciphers spatial distribution of mRNA transcripts at single cell level by integrating single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics data to infer mixture of cell types of spots in slices. Current algorithms are criticized for neglecting connection between scRNA-seq and spatial transcriptomics data, as well as time-consuming, hampering their application to large-scale datasets. RESULTS: In this study, we propose a joint learning nonnegative matrix factorization algorithm for fast cell type deconvolution (aka jMF2D), which integrates scRNA-seq and spatial transcriptomics data with network models. To bridge scRNA-seq and spatial transcriptomics data, jMF2D jointly learns cell type similarity network to enhance quality of signatures of cell types, thereby promoting accuracy and efficiency of deconvolution. Experiments demonstrate that jMF2D outperforms state-of-the-art baselines in terms of accuracy by saving about 90% running time on various datasets generated by different platforms. Furthermore, it can also facilitates the identification of spatial domains and bio-marker genes, providing an efficient and effective model for analyzing spatial transcriptomics data. AVAILABILITY AND IMPLEMENTATION: The software is coded using python, and is free available for academic https://github.com/xkmaxidian/jMF2D.

Algorithms

Tc-99m DTPA renal scintigraphy using deconvolution analysis with six functional images of the mean time to evaluate acute pyelonephritis.

In 38 children with proved P-fimbriated Escherichia coli acute pyelonephritis, Tc-99m DTPA dynamic renal scintigraphy in the zoom mode using deconvolution analysis was performed, and the results were compared with those of Tc-99m DMSA scans. From the dynamic study, six functional images of the mean time were generated. Each functional image was analyzed separately to search for focal areas of increased mean time within the kidney contour, especially over the kidney parenchyma. Time-activity curves from these areas were generated and analyzed. Tc-99m DMSA scintigraphy showed generalized or focal decreased uptake in 32 (41.8%) kidneys, and deconvolution analysis of Tc-99m DTPA scintigraphy revealed pathologic renographic curves in 58 (77.6%) kidneys. Prolonged whole-kidney and normal renal parenchymal transit times (dilatation without obstruction) were found in 38 (50%) kidneys, whereas prolonged whole-kidney and renal parenchymal transit times (dilatation with obstruction) were observed in 20 (27.6%) kidneys. Separate analysis of each of the six functional images of the mean time showed focal areas of increased mean time in the kidney parenchyma of 11 kidneys. In five cases, time-activity curves from these areas showed a sharp increase of activity on the descending part of the curve, which might reflect the return of urine from the collecting system into kidney cortex (i.e., intrarenal reflux). These results showed that in a urinary tract with acute pyelonephritis, urodynamic changes may lead to obstructive nephropathy and intrarenal reflux. Tc-99m DTPA renal scintigraphy in the zoom mode using deconvolution analysis with six functional images of the mean time has proved to be a valuable method to evaluate acute pyelonephritis, thus allowing dynamic and morphologic analysis of the urinary tract at the same time.

Child

In vitro and in vivo deconvolution assessment of drug release kinetics from oxprenolol Oros preparations.

The relationship between in vitro and in vivo drug release from Oros systems has been examined by analysing plasma concentration data from two pharmacokinetic studies, using a numerical deconvolution technique. This method generates an input profile by comparing the response with that achieved following an instantaneous reference unit dose. The approach is conceptually simple and does not require compartmental pharmacokinetic modelling or curve fitting. In the analysis of the first study, the plasma profile following intravenous dosing was used as the reference function, allowing the combined release/absorption process to be calculated; for the second, an oral bolus was used, the result of the deconvolution therefore indicating the in vivo dissolution rate of the Oros systems. The in vivo release from Oros in most volunteers followed the same pattern as that measured in vitro; only after 6-8 h was the decline in the in vivo release rate somewhat greater than expected. In a few individuals the cumulative absorption profile reached an early plateau level which coincided, on some but not all occasions, with the premature excretion of the Oros system from the body. The amount of drug in recovered systems agreed reasonably with the prediction of the deconvolution analysis.

Biological Availability

The frequency and amplitude of growth hormone secretory episodes as determined by deconvolution analysis are increased in adolescents with insulin dependent diabetes mellitus and are unaffected by short-term euglycaemia.

OBJECTIVE: High overnight plasma growth hormone (GH) levels in insulin-dependent diabetes mellitus (IDDM) are reflected in both an increase in the GH pulse amplitude and elevated baseline GH concentrations. To determine whether these are a result of an increase in GH secretory episodes, we undertook deconvolution analysis of overnight GH profiles using previously determined half-life data. DESIGN: Deconvolution of overnight GH profiles (2000-0800 h) was undertaken from normal and diabetic adolescents (either on their usual insulin regime (n = 15), during overnight euglycaemic clamp using a variable rate insulin infusion (n = 29), or during clamp plus 100 mg pirenzepine to suppress endogenous GH (n = 7)). PATIENTS: Thirty-five normal and 29 diabetic adolescents of both sexes at all stages of puberty. MEASUREMENTS: GH secretory rates were calculated from deconvolution analysis, and Fourier transformation was increased mean overnight GH secretion when analysed by sex and by puberty stage compared to normal subjects; overnight GH secretion median (range) of diabetic group 1.88 (0.56-3.81) mU/min; control group 0.62 (0.32-1.92) mU/min (P < 0.001). Fourier transform analysis of these secretory episodes showed greater pulse frequency in the diabetics with dominant pulse periodicity of 90 minutes compared with 135 minutes in normal subjects. During overnight euglycaemia, mean +/- SEM overnight GH secretory rates were comparable to subjects' usual regime night (1.82 +/- 0.33 vs 1.91 +/- 0.37 mU/min) and there was no change in the dominant pulse periodicity of 90 minutes. Pirenzepine administration in diabetic subjects significantly reduced overnight GH secretion from 1.57 +/- 0.19 to 0.71 +/- 0.80 mU/min (P < 0.001) showing a median (range) reduction of 63 (9.3-82.8)% when compared to the subjects' clamp night. However, dominant pulse periodicity was not altered by pirenzepine administration, and remained at 90 minutes. CONCLUSION: In patients with insulin-dependent diabetes mellitus there is an increase in both the amplitude and frequency of pulsatile GH secretion compared to normal subjects, which is not affected by maintenance of overnight normoglycaemia. The anticholinergic drug pirenzepine appears to suppress the amplitude of GH pulse secretion but has no effect on frequency.

Adolescent

Validation of deconvolutional analysis for the measurement of hepatic function in dogs with toxic-induced liver disease.

The extraction of the hepatobiliary radiopharmaceutical 99mTc-mebrofenin (Choletec) by the liver can be used to evaluate the severity of hepatocellular disease. The hepatic parenchymal cells extract mebrofenin from the blood by the same active transport mechanism as bilirubin. The ability of the liver to extract 99mTc-mebrofenin is a measure of hepatic parenchymal cell function. In this study, we induced hepatocellular disease by administration of a hepatotoxic drug and compared a direct method of determining the hepatic extraction of 99mTc-mebrofenin to hepatic extraction fraction derived from deconvolutional analysis. We also compared both methods of calculating the hepatic extraction of 99mTc-mebrofenin to liver histopathology. Hepatic extraction fraction derived from deconvolutional analysis correlated very well to the direct measurement technique (R=0.922, p < 0.001). Both methods of determining hepatic extraction correlated well to quantitative histopathology, having the same correlation coefficient and p values. (R=-0.833, p=0.003). As the hepatic extraction 99mTc-mebrofenin decreased, the severity of the histopathologic lesions of the liver increased in a linear fashion. There was a significant correlation of the hepatic excretion T1/2 to quantitative histopathology (R=0.949, p < 0.001). The hepatic excretion T1/2 increased as the severity of the histopathologic lesions of the liver increased. Hepatic extraction (HEF) and excretion of 99mTc-mebrofenin are good predictors of the severity of hepatocellular damage in toxic induced liver disease. This study helps validate the premise that HEF derived from deconvolutional analysis is a good predictor of the actual first pass hepatic extraction of 99mTc-mebrofenin.

Aniline Compounds

Extraction of pencil beam kernels by the deconvolution method.

A method has been developed to extract pencil beam kernels from measured broad beam profiles. In theory, the convolution of a symmetric kernel with a step function will yield a function that is symmetric about the inflection point. Conversely, by deconvolution, the kernel may be extracted from a measured distribution. In practice, however, due to the uncertainties and errors associated with the measurements and due to the singularities produced in the fast Fourier transforms employed in the deconvolution process, the kernels thus obtained and the dose distributions calculated therefrom, often exhibit erratic fluctuations. We propose a method that transforms measured profiles to new, modified distributions so that they satisfy the theoretical symmetry condition. The resultant kernel from the deconvolution is then free of fluctuations. We applied this method to compute photon and electron dose distributions at various depths in water and electron fluence distributions in air. The agreement between measured and computed profiles is within 1% in dose or 1 mm in distance in high dose gradient regions.

Fourier Analysis

The use of deconvolution and total least squares in recovering a radiation detector line spread function.

We present a method for obtaining the line spread function (LSF) of any radiation detector from measured data. The problem of finding a LSF is essentially a discrete deconvolution from known values of the input (Monte Carlo generated data) and the output (measured data) which can be put into matrix form. We applied the total least squares (TLS) method which is particularly useful when there are errors in both the input and output data. Results from computer simulation as well as from actual data are shown. In a practical application, however, our technique is currently limited by the ability of the Monte Carlo data to simulate correctly the inherent data from the head of the linear accelerator (linac). To overcome this difficulty we have solved by deconvolution and TLS for a more realistic inherent beam profile of our linac using the information from both profile data as measured with film and the film densitometer response function. The LSF of the densitometer was estimated with a simple method of direct measurement of a slit image and a full width at half maximum (FWHM) of 0.997 mm was recorded. Additionally, using the knowledge of this realistic inherent profile of the linac, a blurring function representing the finite source size effect missing in our current Monte Carlo profile simulation was determined. Finally, with the realistic inherent beam profile we have applied the deconvolution and TLS method to find a LSF for the Markus chamber and found a resulting FWHM of 5.39 mm. The TLS approach for deconvolving can find a useful application for both finding the LSF and correcting for the detector size effect once its LSF is known. This type of correction is required when a high spatial resolution is needed (e.g., in small field off-axis measurements). Convolved and measured profiles are also presented to illustrate the effect of the blurring due to different LSFs.

Biophysical Phenomena

Reconstructing the rate of appearance of subcutaneous insulin by deconvolution.

In this paper a deconvolution scheme is presented to reconstruct the rate of appearance of subcutaneously injected insulin. Relevant aspects of experiment design are briefly described. Intravenous insulin kinetics are modeled to determine the impulse response of the system. The deconvolution problem is not ill conditioned and is solved using a least-squares method without imposing constraints on the input. An estimate of the error of the reconstructed input is provided. The reliability of the deconvolution scheme is tested by means of an independent validation study. Finally, the different sources of error that affect the method are discussed, and a figure of the global error is derived.

Humans

Hydrocortisone secretion: production rate and pulse characterization by numerical deconvolution.

Based on serial blood sampling over 24 h, hydrocortisone was shown to be secreted episodically in the horse. The purpose of the present experiment was to characterize peaks and troughs by analyzing the instantaneous secretion rate profile obtained by a deconvolution technique rather than from the plasma concentration time profile. Kinetic parameters of hydrocortisone were determined following intravenous bolus and intravenous perfusion of hydrocortisone. Stationary and nonlinearity of hydrocortisone disposition were demonstrated. With the use of clearance values calculated from constant perfusion administration, the 24-h hydrocortisone production rate was estimated at 0.46 +/- 0.08 mg.kg-1.24 h-1. The instantaneous secretory profile was reconstituted by deconvoluting the plasma concentration profile using structural parameters determined from the bolus hydrocortisone administration. When this secretory profile was subjected to a pulse analysis program, the number of detected peaks was found to be 17.25 +/- 1.26 and the mean peak duration 34.01 +/- 5.52 min. The total duration of secretory activity was estimated at 582.5 +/- 63.97 min. By comparison, when the plasma concentration profile was analyzed directly, the number of peaks was only 10.0 +/- 1.41 but their mean duration was much longer, i.e., 105.25 +/- 21.24 min. The origin of these differences and the advantages and limits of deconvolution analysis are discussed.

Animals

Impact of sampling technique on appraisal of pulsatile insulin secretion by deconvolution and cluster analysis.

Little is known about the optimal experimental conditions for assessing pulsatile insulin secretion in vivo. To address this, we employed a recently validated canine model (n = 12) to determine the consequences of 1) sampling from the systemic circulation (SC) vs. the portal vein (PV), 2) sampling intensity and duration, and 3) deconvolution vs. cluster analysis on assessing pulsatile insulin secretion. PV vs. SC sampling resulted in a approximately 40% higher pulse frequency by deconvolution (9.0 +/- 0.5 vs. 6.6 +/- 0.9 pulses/h, P < 0.02) and cluster analysis (7.5 +/- 0.3 vs. 5.6 +/- 0.6 pulses/h, P < 0.01) due to a higher signal-to-noise ratio (19 +/- 4.8 PV vs. 12 +/- 1.8 SC). PV sampling also disclosed a higher calculated contribution of the pulsatile vs. nonpulsatile mode of delivery to total insulin secretion (57 +/- 4 vs. 28 +/- 5%, P < 0.001). Analysis of the relevance of sampling intensity revealed that 1-min data yielded a markedly higher estimate of pulse frequency with PV sampling than 2-min data (9.0 +/- 0.5 vs. 5.4 +/- 0.5, P < 0.02, deconvolution; 7.5 +/- 0.3 vs. 4.3 +/- 0.6 pulses/h, P < 0.001, cluster). Optimal sampling duration was shown to be 40 min or more. We conclude that the resolving power of the analytical tool, the anatomic site of blood withdrawal, the frequency of blood sampling, and the duration of the total observation interval all significantly influence estimated insulin secretory pulse frequency and the fraction of insulin secreted in pulses. With the assumption that PV 1-min insulin data constitute the "gold standard," our in vivo inferences of 7.5-9.0 insulin pulses/h closely recapitulate in vitro islet secretory activity.

Animals

Glucose production during an IVGTT by deconvolution: validation with the tracer-to-tracee clamp technique.

Recently, a new method, based on a two-compartment minimal model and deconvolution [A. Caumo and C. Cobelli. Am. J. Physiol 264 (Endocrinol. Metab. 37): E829-E841, 1993; P. Vicini, G. Sparacino, A. Caumo, and C. Cobelli. Comput. Meth. Prog. Biomed. 52: 147-156, 1997], has been proposed to estimate endogenous glucose production (EGP) from labeled intravenous glucose tolerance test (IVGTT) data. Our aim here is to compare this EGP profile with that independently obtained with the reference method, based on the tracer-to-tracee ratio (TTR) clamp. An insulin-modified (0.03 U/kg body wt infused over 5 min) [6,6-2H2]glucose-labeled IVGTT (0.33 g/kg of glucose) was performed in 10 normal subjects. A second tracer ([U-13C]glucose) was also infused during the test in a variable fashion to clamp endogenous glucose TTR. The TTR clamp was quite successful. As a result, the EGP profile, reconstructed from [U-13C]glucose data with the models of Steele and Radziuk, were almost superimposable. The deconvolution-obtained EGP profile, calculated from [6,6-2H2]glucose data, showed remarkable agreement with that obtained from the TTR clamp. Some differences between the two profiles were noted in the estimated basal EGP and in the initial modalities of EGP inhibition. A high interindividual variability was also observed with both methods in the resumption of EGP to baseline; variability was high in both the timing and the extent of resumption. In conclusion, the use of the two-compartment minimal model of the IVGTT and deconvolution allows the estimation of a profile of EGP that is in very good agreement with that independently obtained with a TTR clamp.

Adult

Model-free numerical deconvolution of recirculating indicator concentration curves.

This paper investigates two model-free methods for numerical deconvolution of recirculating indicator concentration curves. The two methods, damped least squares and discrete orthogonal polynomial deconvolution, are applied to simulated data to verify the reliability of the algorithms. Both deconvolution methods provide damping that results in estimated transport functions that are smooth and reasonable estimates of the actual simulated transport function. On convolution with the simulated input curve, the estimated transport functions provide good fits to the simulated output curve. In addition, methods for identifying an optimal solution and for truncating the artifactually long oscillatory tails of the estimated transport functions are proposed, which appear to allow for reasonably accurate estimation of the mean transit times and variances of the transport functions as well. When either method was applied to indicator dilution data obtained from the pulmonary artery and left atrium, it was computationally stable while producing transport functions that when convolved with the input concentration curves provided good fits to the output concentration curves. The combined simulation and experimental results suggest that the proposed methods should be useful for estimating circulation transport functions from indicator dilution data.

Algorithms

Porcine and human insulin absorption from subcutaneous tissues in normal and insulin-dependent diabetic subjects: a deconvolution-based approach.

The mechanisms of sc insulin absorption are not understood, and models for interpreting in vivo data cannot be developed without gross simplification. To overcome this difficulty we developed a new approach which makes use of deconvolution analysis and does not require any model of the sc tissue. In five normal subjects and seven insulin-dependent diabetic (IDDM) patients endogenous insulin secretion was suppressed by means of a hypoglycemic glucose clamp procedure (approximately 2.8 mmol/L) sustained by a continuous insulin infusion (approximately 4 pmol/min.kg). A bolus injection of insulin (5.4 nmol) was administered iv, and plasma insulin concentrations were measured frequently for 2 h to assess iv insulin kinetics. Insulin then was injected sc in the abdominal region, and plasma insulin concentrations were measured for 8 h. Each subject was studied twice, with porcine and semisynthetic human insulin (Actrapid, Novo). The rate of insulin absorption was reconstructed by deconvolution from the plasma concentrations and iv insulin kinetic data. Linearity of the iv insulin kinetics, essential for deconvolution analysis, was confirmed by a dose-response study in the range of the measured concentrations (150-1800 pmol/L). In most instances, a two-compartment model was adequate to describe the iv response. The mean plasma insulin clearance rates were 15.5 +/- 1.9 (+/- SD) mL/min.kg (porcine) and 17.2 +/- 6.0 (human) in normal subjects and 20.7 +/- 8.8 (porcine) and 20.9 +/- 9.1 (human) in the IDDM patients. The rate of appearance of human insulin from sc tissue was faster than that of porcine insulin in both normal and IDDM subjects, but no significant differences were found in bioavailability, which was 55 +/- 12% (+/- SD; porcine) and 61 +/- 34% (human) in the normal subjects, and 84 +/- 28% (porcine) and 86 +/- 23% (human) in the IDDM patients. The rate of absorption and bioavailability were higher in the IDDM patients than in the normal subjects, a difference possibly related to increased sc blood flow in the IDDM patients. No differences were found with regard to glucose requirement values, normalized to plasma insulin concentrations, in agreement with the finding that the bioavailability of the two insulin species was similar.

Adolescent

Deconvolution of emission tomographic data: a clinical evaluation.

A method of improving the quality of images in single photon emission computed tomography (SPECT) is demonstrated using transaxial images of the liver and brain. Deconvolution of the nuclear medicine data by a point source response function (PSRF) acquired previously in a scattering medium attempts to compensate for scattered radiation within the patient. The average geometric response of the collimator of the gamma camera is also compensated for with this technique. Three patients with known metastatic lesions in the liver and three with primary lesions in the brain were imaged. Clinical assessment of reconstructed slices both before and after deconvolution demonstrates that compensating for the effects of scatter and of collimator blurring leads to enhanced detail of pathological lesions. In all cases, cold lesions seen prior to deconvolution were enhanced in detail and, in addition, new lesions were seen with this technique.

Adult

Robust, noniterative, and computationally efficient modification of van Cittert deconvolution optical figuring.

A modification of van Cittert deconvolution (VCD) is introduced and shown to yield a robust, noniterative (or closed-form), and numerically efficient method of deconvolution. This modification removes the restrictions limiting the applicability of conventional VCD only to shapes and relative positions of the convolved functions for which it converges, while also avoiding the ill effects of zeros in these functions. The resulting method is computationally efficient because it is noniterative and uses the fast Fourier transform. In contrast to the convergences obtained with VCD, those obtained with this modified method are ensured by their expansion in terms of an introduced auxiliary function rather than the convolved functions. This permits both the general removal of the above limitations and arbitrarily accurate deconvolution of infinitely sampled input data even in the presence of input data noise. For discretely sampled input data the accuracy of this modification is shown to be limited only by the implicit bandwidth of the input data density. To exemplify its numerical and analytical advantages, I apply the method to computer control of optical surface figuring. I also demonstrate an intrinsic means of optimal frequency filtering of raw input data made available by this modification. The advantages of this procedure are also applicable to image restoration.

Computer Simulation

Optimizing deconvolution techniques by the application of the Münchhausen meta algorithm.

A deconvolution applied to disturbed data often gives poor results, due to fundamental difficulties associated with ill-posed problems. Many numerical and theoretical methods have been invented to circumvent this phenomenon. Their performance varies, depending on the given problem and data. The main aim of this paper is to provide a decision rule for choosing a method for deconvolution and application of this method to the same data. We have called this meta-algorithm Münchhausen. In this paper we introduce and describe for the first time the basic principle of artificial disturbance of the data in the set-up of deconvolution. We demonstrate some interesting features of the random procedure Münchhausen, such as the non parametric set-up, robustness to disturbance of the data and last but not least good performance.

Algorithms

Deconvolution study of the absorption rate and disposition kinetic values of lindane in sheep.

Absorption rate and plasma and fat disposition of lindane after various lindane percutaneous treatments in shorn and unshorn sheep were investigated. To analyze data with a deconvolution method, IV administration was performed to determine the basic pharmacokinetic values of lindane in sheep. After IV administration, the steady state volume of distribution was very high (8.07 +/- 3.60 L/kg of body weight), and the mean residence time was long (28.1 +/- 11.7 hours). Deconvolution analysis indicated that lindane absorption was continuous until 33 to 41 days after spraying with a 0.025% lindane solution. Total amount of absorbed lindane in shorn (15,171 +/- 4,463 micrograms/kg) sheep was about twice that in unshorn (7,615 +/- 3,128 micrograms/kg) sheep; from deconvolution analysis, it was calculated that the time required for 50% of the available dose to be absorbed was between 115 and 179 hours. After percutaneous lindane administration, the fat concentration was compared with the available lindane dose. The apparent half-life of lindane elimination in fat was 225 +/- 47.4 hours, which is similar to the value calculated for the absorption rate constant. By comparing fat and plasma concentrations, it was calculated that for a mean plasma concentration of 5 ng/ml, the fat lindane concentration was 1.65 +/- 0.87 micrograms/g (ie, lower than the generally accepted tolerance level of 2 micrograms/g).

Adipose Tissue