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At least 127 records · Page 7Linked to original sources
PubMed2003

Semi-empirical correction algorithm for AC-9 measurements in a coccolithophore bloom.

Values for the coefficients of absorption (a) and attenuation (c) obtained from AC-9 measurements in coccolithophore blooms do not provide satisfactory inputs for radiance transfer models. We have therefore modified the standard AC-9 scattering correction algorithm by including an extra term, F(lambda, lambda(r)), which allows for possible wavelength dependence in the scattering phase function. We estimated the magnitude of F(lambda, lambda(r)), which is unity in the standard algorithm, by adjusting the absorption and scattering values in Hydrolight radiance transfer calculations until the depth profiles of downward irradiance (E(d)) and upward radiance (L(u)) matched those measured in situ. The modified algorithm was tested with data from a phytoplankton bloom dominated by the coccolithophore Emiliania huxleyi, which occurred in the western English Channel in May 2001. In this paper, we only have sufficient data to adequately constrain the radiance transfer model in one wave band centered on 488 ma. A single value of F(lambda, lambda(r)) = 1.4 was found to produce satisfactory agreement between modeled and observed profiles at four widely spaced stations within the bloom. Measurements of the ratio of backscattering (b(b)) to total scattering (b) showed significant wavelength dependence at these stations.

Journal Article↗
PubMed2001

Computer algorithms for the automated measurement of retinal arteriolar diameters.

AIMS: Quantification of retinal vascular change is difficult and manual measurements of vascular features are slow and subject to observer bias. These problems may be overcome using computer algorithms. Three automated methods and a manual method for measurement of arteriolar diameters from digitised red-free retinal photographs were compared. METHODS: 60 diameters (in pixels) measured by manual identification of vessel edges in red-free retinal images were compared with diameters measured by (1) fitting vessel intensity profiles to a double Gaussian function by non-linear regression, (2) a standard edge detection algorithm (Sobel), and (3) determination of points of maximum intensity variation by a sliding linear regression filter (SLRF). Method agreement was analysed using Bland-Altman plots and the repeatability of each method was assessed. RESULTS: Diameter estimations obtained using the SLRF method were the least scattered although diameters obtained were approximately 3 pixels greater than those measured manually. The SLRF method was the most repeatable and the Gaussian method less so. The Sobel method was the least consistent owing to frequent misinterpretation of the light reflex as the vessel edge. CONCLUSION: Of the three automated methods compared, the SLRF method was the most consistent (defined as the method producing diameter estimations with the least scatter) and the most repeatable in measurements of retinal arteriolar diameter. Application of automated methods of retinal vascular analysis may be useful in the assessment of cardiovascular and other diseases.

Adult↗
PubMed1994

Midplane dose determination using in vivo dose measurements in combination with portal imaging.

The possibility of using portal films in combination with semiconductor in vivo measurements for midplane dose distribution is investigated. A general algorithm, using measured entrance and exit doses and available beam data of the Linac, is proposed to derive the midplane dose for symmetrical inhomogeneities. Experimental verification of the algorithm with phantom measurements is performed for different kinds of inhomogeneities (Al, air and cork) and phantom thicknesses from 13 cm to 30 cm. When using only the entrance dose and the exit dose, provided by the diodes on the beam axis, the algorithm predicts for the different inhomogeneities midplane doses in all cases within 1% of the midplane doses measured with an ionization chamber. When using the portal film in combination with entrance and exit dose measurements to estimate the midplane dose in an off-axis position, the calculated midplane doses are within 3% of the midplane doses measured with an ionization chamber. The midplane doses calculated with the algorithm are compared to the midplane doses obtained with simplified calculation methods, i.e. the arithmetical mean and the geometrical mean of the measured entrance and exit doses. The geometrical mean especially seems to give acceptable results (within 5%) and can as such be used as an easy rule of thumb to estimate roughly the midplane dose. Finally, critical considerations on the validity and the precision of the proposed algorithm are given. The present results confirm the possibility of using the portal film for midplane dose distribution determination at the patient level.

Algorithms↗
PubMed2006

Absolute myoglobin quantitation in serum by combining two-dimensional liquid chromatography-electrospray ionization mass spectrometry and novel data analysis algorithms.

To measure myoglobin, a marker for myocardial infarction, directly in human serum, two-dimensional liquid chromatography in combination with electrospray ionization mass spectrometry was applied as an analytical method. High-abundant serum proteins were depleted by strong anion-exchange chromatography. The myoglobin fraction was digested and injected onto a 60 mm x 0.2 mm i.d. monolithic capillary column for quantitation of selected peptides upon mass spectrometric detection. The addition of known amounts of myoglobin to the serum sample was utilized for calibration, and horse myoglobin was added as an internal standard to improve reproducibility. Calibration graphs were linear and facilitated the reproducible and accurate determination of the myoglobin amount present in serum. Manual data evaluation using integrated peak areas and an automated multistage algorithm fitting two-dimensional models of peptide elution profiles and isotope patterns to the mass spectrometric raw data were compared. When the automated method was applied, a myoglobin concentration of 460 pg/microL serum was determined with a maximum relative deviation from the theoretical value of 10.1% and a maximum relative standard deviation of 13.4%.

Algorithms↗
PubMedDate not supplied

An electronically collimated gamma camera for single photon emission computed tomography. Part II: Image reconstruction and preliminary experimental measurements.

Iterative algorithms have been investigated for reconstructing images from data acquired with a new type of gamma camera based upon an electronic method of collimating gamma radiation. The camera is composed of two detection systems which record a sequential interaction of the emitted gamma radiation. Coincident counting in accordance with Compton scattering kinematics leads to a localization of activity upon a multitude of conical surfaces throughout the object. A two-stage reconstruction procedure in which conical line projection images as seen by each position sensing element of the first detector are reconstructed in the first stage, and tomographic images are reconstructed in the second stage, has been developed. Computer simulation studies of both stages and first-stage reconstruction studies with preliminary experimental data are reported. Experimental data were obtained with one detection element of a prototype germanium detector. A microcomputer based circuit was developed to record coincident counts between the germanium detector and an uncollimated conventional scintillation camera. Point sources of Tc-99m and Cs-137 were used to perform preliminary measurements of sensitivity and point spread function characteristics of electronic collimation.

Models, Structural↗
PubMed2005

Reconstruction of stochastic nonlinear dynamical models from trajectory measurements.

An algorithm is presented for reconstructing stochastic nonlinear dynamical models from noisy time-series data. The approach is analytical; consequently, the resulting algorithm does not require an extensive global search for the model parameters, provides optimal compensation for the effects of dynamical noise, and is robust for a broad range of dynamical models. The strengths of the algorithm are illustrated by inferring the parameters of the stochastic Lorenz system and comparing the results with those of earlier research. The efficiency and accuracy of the algorithm are further demonstrated by inferring a model for a system of five globally and locally coupled noisy oscillators.

Journal Article↗
PubMed2004

A fuzzy relational clustering algorithm based on a dissimilarity measure extracted from data.

One of the critical aspects of clustering algorithms is the correct identification of the dissimilarity measure used to drive the partitioning of the data set. The dissimilarity measure induces the cluster shape and therefore determines the success of clustering algorithms. As cluster shapes change from a data set to another, dissimilarity measures should be extracted from data. To this aim, we exploit some pairs of points with known dissimilarity value to teach a dissimilarity relation to a feed-forward neural network. Then, we use the neural dissimilarity measure to guide an unsupervised relational clustering algorithm. Experiments on synthetic data sets and on the Iris data set show that the relational clustering algorithm based on the neural dissimilarity outperforms some popular clustering algorithms (with possible partial supervision) based on spatial dissimilarity.

Journal Article↗
PubMedDate not supplied

A geometric model for measurement of surface distance, surface area, and volume from tomographic images.

Surface area and volume are essential measurements in the morphometric assessment of anatomical structures. New algorithms were developed to measure (1) distance along a curve, (2) surface area, and (3) volume using data extracted from tomographic images as a geometrical surface model. The model is a list of coordinates and normal vectors for each voxel or point gathered from the surface of a selected object. The resulting surface-based pointlist is also used for high-speed rendering of surfaces. Differential arclength and surface area are measured with high numeric precision by using the absolute value of the maximum component of the unit normal vector (MUNC) to approximate their values. These differential values are summed to measure distance along a curve and surface area. A discrete form of the Divergence theorem, also using the MUNC, is used to calculate volume. The intrinsic accuracy of the measurement algorithms was evaluated using computer generated pointlists of circles, ellipses, spheres, and ellipsoids. Compared to standard measurement techniques, the new algorithms provided the greatest accuracy and least shape-related bias for measurement of distance, surface area, and volume. Feasibility of using the new algorithms to measure physical objects was tested with CT images of spherical, egg-shaped, and irregular shaped objects. The Dividing Cubes algorithm was used to segment and create pointlists from the CT data. Volume and surface area measurements from CT data compared extremely well with reference values for most objects tested (errors less than 2%).

Algorithms↗
PubMed2005

Phase-shifting interferometry with equal phase steps by use of a frequency-tunable diode laser and a Fabry-Perot cavity.

A phase-shifting interferometry (PSI) with equal phase steps by use of a frequency-tunable diode laser and a Fabry-Perot cavity is proposed for the Carré algorithm. The measurement accuracy of the Carré algorithm depends on the equality of the phase steps. Using the Fabry-Perot cavity as a highly stable optical frequency reference, a high degree of phase step equality can be realized in PSI with an optical frequency shift. Our experimental scheme realizes an optical frequency step equality higher than 5.1 x 10(-5) and a measurement repeatability of lambda/800.

Journal Article↗
PubMed1999

Analysis of functional magnetic resonance imaging data using self-organizing mapping with spatial connectivity.

Commonly used methods in analyzing functional magnetic resonance imaging (fMRI) data, such as the Student's t-test and cross-correlation analysis, are model-based approaches. Although these methods are easy to implement and are effective in analyzing data obtained with simple paradigms, they are not applicable in situations in which patterns of neuronal response are complicated and when fMRI response is unknown. In this work, Kohonen's self-organizing mapping (SOM), which is a model-free approach, is adapted for analyzing fMRI data. Because spatial connectivity is an important function in the identification of activation sites in functional brain imaging, it is incorporated into the SOM algorithm. Receiver operating characteristic analysis on simulated data shows that the new algorithm achieves measurable improvement over the standard algorithm. The applicability of the new algorithm is demonstrated on experimental data.

Algorithms↗
PubMed1991

Interinstitutional experience in verification of external photon dose calculations.

Under the auspices of NCI contracts, four institutions have collaborated to assess the accuracy of the pixel-based dose calculation methods they employ for external photon treatment planning. The approach relied on comparing calculations using each group's algorithm with measurements in phantoms of increasing complexity. The first set of measurements consisted of ionization chamber measurements in water phantoms in normally incident square fields, an elongated field, a wedged field, a blocked field, and an obliquely incident beam. The second group of measurements was carried out using thermoluminescent dosimeters in phantoms designed to investigate the effects of surface curvature, high density heterogeneities, and low density heterogeneities. The final study tested the entire treatment planning system, including CT data conversion, in an anthropomorphic phantom. Overall, good agreement between calculation and measurements was found for all algorithms. Regions in which discrepancies were observed are pointed out, areas for algorithm improvement are identified and the clinical import of algorithm accuracy is discussed.

Humans↗
PubMed2004

Multivariate entropy distance method for prokaryotic gene identification.

A new simple method is found for efficient and accurate identification of coding sequences in prokaryotic genome. The method employs a Shannon description of artificial language for DNA sequences. It consists in translating a DNA sequence into a pseudo-amino acid sequence with 20 fundamental words according to the universal genetic code. With an entropy-density profile (EDP), the method maps a sequence of finite length to a vector and then analyzes its position in the 20-dimensional phase space depending on its nature. It is found that the ratio of the relative distance to an averaged coding and non-coding EDP over a small number (up to one) of open reading frames (ORFs) can serve as a good coding potential. An iterative algorithm is designed for finding a set of "root" sequences using this coding potential. A multivariate entropy distance (MED) algorithm is then proposed for the identification of prokaryotic genes; it has a feature to combine the use of a coding potential and an EDP-based sequence similarity analysis. The current version of MED is unsupervised, parameter-free and simple to implement. It is demonstrated to be able to detect 95-99% genes with 10-30% of additional genes when tested against the RefSeq database of NCBI and to detect 97.5-99.8% of confirmed genes with known functions. It is also shown to be able to find a set of (functionally known) genes that are missed by other well-known gene finding algorithms. All measurements show that the MED algorithm reaches a similar performance level as the algorithms like GeneMark and Glimmer for prokaryotic gene prediction.

Algorithms↗
PubMed2004

Multi-detector row computed tomography of the heart: does a multi-segment reconstruction algorithm improve left ventricular volume measurements?

A multi-segment cardiac image reconstruction algorithm in multi-detector row computed tomography (MDCT) was evaluated regarding temporal resolution and determination of left ventricular (LV) volumes and global LV function. MDCT and cine magnetic resonance (CMR) imaging were performed in 12 patients with known or suspected coronary artery disease. Patients gave informed written consent for the MDCT and the CMR exam. MDCT data were reconstructed using the standard adaptive cardiac volume (ACV) algorithm as well as a multi-segment algorithm utilizing data from three, five and seven rotations. LV end-diastolic (LV-EDV) and end-systolic volumes and ejection fraction (LV-EF) were determined from short-axis image reformations and compared to CMR data. Mean temporal resolution achieved was 192+/-24 ms using the ACV algorithm and improved significantly utilizing the three, five and seven data segments to 139+/-12, 113+/-13 and 96+/-11 ms (P<0.001 for each). Mean LV-EDV was without significant differences using the ACV algorithm, the multi-segment approach and CMR imaging. Despite improved temporal resolution with multi-segment image reconstruction, end-systolic volumes were less accurately measured (mean differences 3.9+/-11.8 ml to 8.1+/-13.9 ml), resulting in a consistent underestimation of LV-EF by 2.3-5.4% in comparison to CMR imaging (Bland-Altman analysis). Multi-segment image reconstruction improves temporal resolution compared to the standard ACV algorithm, but this does not result in a benefit for determination of LV volume and function.

Adult↗
PubMed2006

Emissitivity spectra obtained from field and laboratory measurements using the temperature and emissivity separation algorithm.

Surface emissivities play an important role in thermal remote sensing, since knowledge of them is required to estimate land surface temperature with enough accuracy. They are also important in other environmental or geological studies. We show the results obtained for the emissivity spectra of different natural surfaces (water, green, and senescent vegetation) by applying the temperature and emissivity separation (TES) algorithm to ground-based measurements collected at the field with a multiband thermal radiometer. The results have been tested with data included in spectral libraries, and rms errors lower than 0.01 have been found, except for senescent vegetation. Two methods are also proposed to apply the TES algorithm to measurements achieved in the laboratory: (i) by heating the sample and (ii) using a box with reflective walls.

Journal Article↗
PubMed1999

Comparison of methods for instantaneous angiographic blood flow measurement.

Several different algorithms have been reported for measurement of blood flow rates and velocities from digital x-ray angiograms. We compare four videodensitometric methods: (1) distance-density curve matching (DDCM), (2) distance-density curve matching with curve-fitting (DDCM-F), (3) bolus mass tracking with curve-fitting (BMT-F) and (4) fluid continuity method (FCM). We tested the flow algorithms with simulated angiograms and with images obtained from a programmable flow phantom under clinically realistic flow and contrast injection conditions including imperfect mixing. All methods perform well for simulated angiograms. On phantom angiograms with constant flow, all methods tended to underestimate flow velocities by at least 7% and demonstrate high variability between consecutive measurements. The FCM demonstrated relatively low variability, but a large negative bias. The DDCM method was moderately biased and had the highest variability. The BMT-F method demonstrated the lowest bias (-7.1%) and the lowest variability both within (27%) and between (27%) studies. No method yields reliable measurements near the peak contrast opacification, when little or no gradient of contrast is present. The extrapolating version of the BMT-F method was also the most robust for estimation of interframe displacements longer than the field of view.

Algorithms↗