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An empirically based model of the electrically evoked compound action potential.

The relationship between electrically evoked single-fiber action potentials and the electrically evoked compound action potential of the auditory nerve is of interest to those attempting to model such responses with computational techniques. It also relates to efforts to exploit the gross potentials that can now be recorded by some implantable cochlear prostheses. In this paper, we develop a computational model of the auditory nerve response to single, pulsatile, electrical stimuli based upon the response characteristics obtained from 230 single fibers of 13 cats. These fibers were stimulated by brief (39s) monophasic cathodic stimuli delivered by a monopolar intracochlear electrode. The data were pooled to obtain an estimate of the distribution of fiber thresholds. Post-stimulus time histograms were modeled using Poisson functions and adjusted to account for empirically determined latency and jitter characteristics. The probabilistic nature of single-fiber input-output functions (i.e. Verveen's (1961) 'relative spread') was also modelled. PST histograms from 5000 modelled fibers were then summed and convolved with an estimated 'unit potential' following the method of Goldstein and Kiang (1958). This convolution produced modelled compound action potentials, which were then compared with experimentally obtained data. Manipulations of model parameters affecting threshold, jitter, and relative spread suggest that the most important determinant of the shape of the EAP amplitude-level function is the threshold distribution. A model based solely on threshold distribution produces an EAP input-output function similar to one that accounts for probabilistic single-fiber input-output functions. Discrepancies between these two models do occur if the threshold distribution function is compressed significantly, as might be the case in pathological cochleae with altered distributions or numbers of nerve fibers.

Algorithms↗

Comparative evaluation of JPEG and JPEG2000 compression in quantitative digital subtraction radiography.

OBJECTIVES: The aim of this in vitro study was to compare the impact of JPEG and the novel JPEG2000 compression standard on quantitative digital subtraction radiography (DSR) and to determine the acceptable JPEG2000 compression ratios for DSR. METHODS: Nine dry pig mandible sections were radiographed three times ('Baseline', 'No change', and 'Gain') with standardized projection geometry. Bone gain was simulated by adding artificial bone chips (1, 4 and 15 mg). Images were registered, compressed by JPEG and JPEG2000 using compression ratios (CR) of 1 : 7, 1 : 16, 1 : 22, and 1 : 31, and then subtracted. Image distortion was assessed objectively by calculating average pixel error and peak signal to noise ratio. No change areas in compressed and subtracted 'No change-Baseline' images and bone gain volumes in compressed and subtracted 'Gain-Baseline' images were calculated for both compression standards and compared. RESULTS: JPEG introduced less distortion at low CRs, while JPEG2000 was superior at higher CRs. At CR of 1 : 7, no significant difference between JPEG and JPEG2000 was found. JPEG2000 yielded better results for no change measurements at higher CRs. Volumes of simulated bone gain were overestimated when JPEG and underestimated when JPEG2000 compression was used. CONCLUSIONS: At CR of 1 : 7 JPEG and JPEG2000 performed similarly, which indicates that CR of 1:7 in JPEG2000 can be used for DSR if images are registered before compression. At higher CRs, JPEG2000 is superior to JPEG but image distortions are too high for reliable quantitative DSR.

Algorithms↗

Pattern filtering for detection of neural activity, with examples from HVc activity during sleep in zebra finches.

The detection of patterned spiking activity is important in the study of neural coding. A pattern filtering approach is developed for pattern detection under the framework of point processes, which offers flexibility in combining temporal details and firing rates. The detection combines multiple steps of filtering in a coarse-to-fine manner. Under some conditional Poisson assumptions on the spiking activity, each filtering step is equivalent to classifying by likelihood ratios all the data segments as targets or as background sequences. Unlike previous studies, where global surrogate data were used to evaluate the statistical significance of the detected patterns, a localized p-test procedure is developed, which better accounts for firing modulation and nonstationarity in spiking activity. Common temporal structures of patterned activity are learned using an entropy-based alignment procedure, without relying on metrics or pair-wise alignment. Applications of pattern filtering to single, presumptive interneurons recorded in the nucleus HVc of zebra finch are illustrated. These demonstrate a match between the auditory-evoked response to playback of the individual bird's own song and spontaneous activity during sleep. Small temporal compression or expansion, or both, is required for optimal matching of spontaneous patterns to stimulus-evoked activity.

Action Potentials↗

Virtual sonography through the Internet: volume compression issues.

BACKGROUND: Three-dimensional ultrasound images allow virtual sonography even at a distance. However, the size of final 3-D files limits their transmission through slow networks such as the Internet. OBJECTIVE: To analyze compression techniques that transform ultrasound images into small 3-D volumes that can be transmitted through the Internet without loss of relevant medical information. METHODS: Samples were selected from ultrasound examinations performed during, 1999-2000, in the Obstetrics and Gynecology Department at the University Hospital in La Laguna, Canary Islands, Spain. The conventional ultrasound video output was recorded at 25 fps (frames per second) on a PC, producing 100- to 120-MB files (for from 500 to 550 frames). Processing to obtain 3-D images progressively reduced file size. RESULTS: The original frames passed through different compression stages: selecting the region of interest, rendering techniques, and compression for storage. Final 3-D volumes reached 1:25 compression rates (1.5- to 2-MB files). Those volumes need 7 to 8 minutes to be transmitted through the Internet at a mean data throughput of 6.6 Kbytes per second. At the receiving site, virtual sonography is possible using orthogonal projections or oblique cuts. CONCLUSIONS: Modern volume-rendering techniques allowed distant virtual sonography through the Internet. This is the result of their efficient data compression that maintains its attractiveness as a main criterion for distant diagnosis.

Algorithms↗

Discovering simple DNA sequences by compression.

An information-theoretic DNA compression scheme devised by Milosavljevic and Jurka (1993) has been used in many places in the literature for both the discovery of new genes and the compression of DNA. Their compression method applies an encoding of previously occurring runs. They use 5 different code-words: four being the DNA bases, A, C, G and T, and the other being a pointer to a previously occurring run. They advocate a code-word of length log2 5 for each of these and then encoding a run by a code-word of length 2 x log2 n, where n is the length of the sequence. This scheme encodes the start of the sequence with a code-word of length log2 n and likewise encodes the end of the sequence with a code-word of length log2 n. In this paper, we show the above coding scheme to be inefficient in various ways and improve upon it so that it can compress DNA. We discuss our implementation of various schemes some of which run in linear time.

Algorithms↗

Comparison of motion correction algorithms for cardiac SPECT.

UNLABELLED: Patient motion remains a significant source of unsatisfactory cardiac SPECT examinations. The extent to which image recovery can be achieved with correction algorithms is unknown. METHODS: Nine subjects who had completed motion-free redistribution 201Tlcardiac SPECT subsequently underwent simultaneous dual-isotope (201Tl/99mTc) SPECT with a 99mTc cutaneous point source, while the imaging table was subjected to predefined nonreturning y-translation movements. Cardiac reconstructions, marker reconstructions and marker-compressed dynamic images were generated from the raw data after applying the following correction methods: diverging squares, cross-correlation of the cardiac data and cross-correlation of the marker. RESULTS: Marker cross-correlation performed significantly better than all other methods with good-excellent results in all evaluations. This compared with good-excellent results in none of 27 for the raw data, in 13 of 27 for cardiac cross-correlation and in 7 of 27 for diverging squares (p < 10(-5)). The superiority of the marker-based method was confirmed on analysis of bullseye difference maps and quantitation of residual motion in the point-source data. CONCLUSION: Motion artifacts can accurately be detected and corrected using cross-correlation of an external point-source. Furthermore, this technique provides useful independent information on the degree of image recovery.

Algorithms↗

Development and validation of a series of three-dimensional finite element models of the equine metacarpus.

Three-dimensional finite element (FE) models of the left metacarpi of five adult horses were developed from quantitative computed tomography data, using the algorithms of Keyak et al. (1990, J Biomed. Engng 12, 389-397). The metacarpi were then equipped with 12 rosette strain gauges and loaded non-destructively in a mechanical testing machine. The bones and the models were loaded in axial compression, with the load evenly distributed across the distal row of carpal bones, and with a point load placed mediad to the sagittal midline, to a load equivalent to three times body weight (-15 kN); and in sagittal four-point bending to -2 kN. Maximum and minimum principal strains from the models were compared with those at the strain gauge rosettes. There were significant (p < 0.001) and strong (0.69 < r < 0.90) correlations between predicted and observed surface principal strains, most often resolving as second- or third-order polynomial relationships. In most cases, particularly at extreme strain magnitudes, the models tended to overestimate the observed strain magnitudes. These data suggest that the models are robust and accurate predictors of surface strains. Validation of these models lends further support for the use of this method of automated three-dimensional FE modeling, with its emphasis on accurate, individualized portrayal of structural geometry and material distribution, in research applications, and specifically for the use of these models in the study of the biology and mechanics of the equine metacarpus.

Animals↗

Iterative kernel principal component analysis for image modeling.

In recent years, Kernel Principal Component Analysis (KPCA) has been suggested for various image processing tasks requiring an image model such as, e.g., denoising or compression. The original form of KPCA, however, can be only applied to strongly restricted image classes due to the limited number of training examples that can be processed. We therefore propose a new iterative method for performing KPCA, the Kernel Hebbian Algorithm which iteratively estimates the Kernel Principal Components with only linear order memory complexity. In our experiments, we compute models for complex image classes such as faces and natural images which require a large number of training examples. The resulting image models are tested in single-frame super-resolution and denoising applications. The KPCA model is not specifically tailored to these tasks; in fact, the same model can be used in super-resolution with variable input resolution, or denoising with unknown noise characteristics. In spite of this, both super-resolution and denoising performance are comparable to existing methods.

Algorithms↗

Enhanced 3D PET OSEM reconstruction using inter-update Metz filtering.

We present an enhancement of the OSEM (ordered set expectation maximization) algorithm for 3D PET reconstruction, which we call the inter-update Metz filtered OSEM (IMF-OSEM). The IMF-OSEM algorithm incorporates filtering action into the image updating process in order to improve the quality of the reconstruction. With this technique, the multiplicative correction image--ordinarily used to update image estimates in plain OSEM--is applied to a Metz-filtered version of the image estimate at certain intervals. In addition, we present a software implementation that employs several high-speed features to accelerate reconstruction. These features include, firstly, forward and back projection functions which make full use of symmetry as well as a fast incremental computation technique. Secondly, the software has the capability of running in parallel mode on several processors. The parallelization approach employed yields a significant speed-up, which is nearly independent of the amount of data. Together, these features lead to reasonable reconstruction times even when using large image arrays and non-axially compressed projection data. The performance of IMF-OSEM was tested on phantom data acquired on the GE Advance scanner. Our results demonstrate that an appropriate choice of Metz filter parameters can improve the contrast-noise balance of certain regions of interest relative to both plain and post-filtered OSEM, and to the GE commercial reprojection algorithm software.

Algorithms↗

The nearest subclass classifier: a compromise between the nearest mean and nearest neighbor classifier.

We present the Nearest Subclass Classifier (NSC), which is a classification algorithm that unifies the flexibility of the nearest neighbor classifier with the robustness of the nearest mean classifier. The algorithm is based on the Maximum Variance Cluster algorithm and, as such, it belongs to the class of prototype-based classifiers. The variance constraint parameter of the cluster algorithm serves to regularize the classifier, that is, to prevent overfitting. With a low variance constraint value, the classifier turns into the nearest neighbor classifier and, with a high variance parameter, it becomes the nearest mean classifier with the respective properties. In other words, the number of prototypes ranges from the whole training set to only one per class. In the experiments, we compared the NSC with regard to its performance and data set compression ratio to several other prototype-based methods. On several data sets, the NSC performed similarly to the k-nearest neighbor classifier, which is a well-established classifier in many domains. Also concerning storage requirements and classification speed, the NSC has favorable properties, so it gives a good compromise between classification performance and efficiency.

Algorithms↗

[Goiter and nodular thyroid disease: clinical guidelines for diagnosis and treatment. (Waiting? Hormone therapy? Surgery? radioiodine?)].

Nodular thyroid disease is a common problem. We present clinical guidelines for the management of patients with thyroid nodules, multinodular goiters and thyroid cysts for use by primary physicians. In the initial evaluation ultrasonography of the thyroid and fine-needle aspiration biopsy (FNAB) is recommended. FNAB has become the cornerstone in the evaluation of solitary thyroid nodules, cysts and dominant nodules within multinodular goiters. If the procedure is done properly, it should have a false-negative rate of less than 5% and a false-positive rate of not more than 1%. Thyroid radionuclide scans are less frequently used in the initial evaluation of a nodular goiter. Surgery is the primary therapy for patients with nodular thyroid disease. Other available treatment options are radioiodine and TSH-suppression with thyroxine. The main indications for surgery in euthyroid patients with thyroid nodule or with nontoxic multinodular goiter are recently documented or suspected malignancy, compression of the trachea and esophagus, significant growth of the nodule, recurrence of a cyst after aspiration, neck discomfort and cosmetic concern.

Algorithms↗

Compressing data volume of left ventricular cineangiograms.

In this paper a method of compressing data volume for left ventricular cineangiograms is proposed. This method enables digital-optical discs to store the cineangiograms with an equivalent recording density to that of HDTV VTR's while preserving the quality of the original image. The data volume of the cineangiograms is compressed by approximating function and storing its coefficients. With this method, each cineangiogram frame is first decomposed into three regions: the inner part, the inner wall, and the background (using a statistical method previously reported by the authors). Each region is then compressed by means of a difference operation and an adaptive approximation with smooth functions. Performance is tested on 20 cases using actual cineangiograms. The specifications were verified for a spatial resolution of 1000 TV lines, a dynamic range of 60 dB, an SNR of 40 dB [pp/rms], volume compression to 7% of the original volume, and 0.19 [second/frame] for decoding on a 1.7 MFLOPS computer.

Algorithms↗

Medical image compression based on a morphological representation of wavelet coefficients.

Image compression is fundamental to the efficient and cost-effective use of digital medical imaging technology and applications. Wavelet transform techniques currently provide the most promising approach to high-quality image compression which is essential for diagnostic medical applications. A novel approach to image compression based on the wavelet decomposition has been developed which utilizes the shape or morphology of wavelet transform coefficients in the wavelet domain to isolate and retain significant coefficients corresponding to image structure and features. The remaining coefficients are further compressed using a combination of run-length and Huffman coding. The technique has been implemented and applied to full 16 bit medical image data for a range of compression ratios. Objective peak signal-to-noise ratio performance of the compression technique was analyzed. Results indicate that good reconstructed image quality can be achieved at compression ratios of up to 15:1 for the image types studied. This technique represents an effective approach to the compression of diagnostic medical images and is worthy of further, more thorough, evaluation of diagnostic quality and accuracy in a clinical setting.

Algorithms↗

The need for standardisation of peak flow charts.

Peak expiratory flow (PEF) monitoring is recommended in asthma guidelines as a tool for assessing severity, monitoring response to treatment, detecting exacerbations, identifying triggers, and providing objective justification for treatment to the patient, but some clinicians have expressed concerns about its relevance in the management of asthma. We have identified a sevenfold variation in the scale of existing PEF charts, with resulting wide variation in the appearance of the same PEF date on different charts. There is an obvious need for standardisation of PEF charts to avoid confusion for patients and to allow development of pattern recognition skills by clinicians. Evidence is provided from visual perception studies to suggest that preference should be given to a horizontally compressed PEF chart to facilitate identification of exacerbations and of overall trends, but this needs to be formally evaluated by retrospective and prospective studies. It is hoped that clinical expertise in PEF pattern recognition can eventually be incorporated into electronic decision making algorithms, as has occurred in occupational asthma, but, in the meantime, the ideal PEF chart for asthma management will represent a compromise between ease of manual data entry and ease of interpretation.

Asthma↗

Detection of subtle abnormalities on chest radiographs after irreversible compression.

PURPOSE: To assess the effect of wavelet-based compression of posteroanterior chest radiographs on detection of small uncalcified pulmonary nodules and fibrosis. MATERIALS AND METHODS: Computed tomography (CT) of the chest was used to identify 20 patients with normal posteroanterior chest radiographs, 20 with a solitary uncalcified pulmonary nodule 1-2 cm in diameter, and 20 with fibrotic disease. A double-blind protocol for readings of original images and images compressed at 40:1 and 80:1 was analyzed by using the nonparametric receiver operating characteristic to measure differences in diagnostic accuracy and their statistical significance. RESULTS: There was no substantial difference in the overall diagnostic accuracy (measured by the area under the curve index) for both nodules and fibrosis between images compressed at 40:1 and 80:1 and uncompressed images. Readers tended to perform better on images compressed at 40:1 compared with uncompressed images. The "high-sensitivity" portion of the 80:1 compression curve for nodules was below that for the uncompressed curve, although this was not statistically significant. CONCLUSION: Lossy compression of chest radiographs at 40:1 can be used without decreased diagnostic accuracy for detection of pulmonary nodules and fibrosis. There is no statistically significant difference in diagnostic accuracy at 80:1 compression, but detection ability is decreased.

Algorithms↗

Digital restoration of defocused images in the wavelet domain.

Many cameras nowadays are equipped with an autofocus mechanism that attempts to take pictures at the best possible focus. However, there are situations in which the pictures are still out of focus, such as when the photographer has mistakenly focused at a wrong position or when the focusing region consists of objects of different depths and therefore confuses the autofocus system. With a digital camera, we can attempt to use digital image-restoration techniques to bring the pictures back into focus. We design an algorithm that restores the image by digitally enhancing the corresponding frequency bands. We employ the restoration in the wavelet domain so that this restoration scheme can be compliant with JPEG 2000, which is positioned to succeed JPEG as the next image-compression standard and has the potential to be widely adopted by the digital photography industry owing to its many advanced features.

Journal Article↗

Registration of three-dimensional compound ultrasound scans of the breast for refraction and motion correction.

Use of multiple look directions, that is, compound imaging, has been shown previously to increase detection of specular reflectors and averaging of speckle noise in gray-scale images, often at the expense of spatial resolution and other misregistration errors. In color flow imaging, additional view angles can fill in vessels missed due to Doppler angle dropout and increase quantitative and visual Doppler accuracy by triangulation or a simple peak-frequency-shift combination algorithm. Image registration and unwarping throughout multiple three-dimensional (3D) volume sets should correct for many refraction artifacts, motion between and during compounded image sets and even, possibly, positioning errors between image sets, acquired months apart, to display growth of abnormalities. The registration described here does not provide sufficient accuracy for formation of enhanced coherent apertures, but shows promise in some cases to provide superior compound images and possibly comparisons of current and prior studies. In this study, the breast is stabilized by mild compression between a flat plate and a scanning membrane. Registration and unwarping is performed retrospectively on two separate volumetric data sets by defining pairs of corresponding points and, in some cases, line and plane segments. Three-dimensional linear affine transforms are performed using identified points, lines and planes. 3D nonlinear warped transforms are also possible given adequate numbers of identifiable points. More than two data sets are registered by selecting one as the standard, and registering the remainder to match. The most appropriate algorithm, such as averaging or maximum amplitude, may be used to combine the data sets for display. Significant success has been achieved in compound display of a test object and of the breast in vivo, even when there was relative motion or warping between image sets. In pulse-echo imaging, homologous feature registration for compounding appears to have advantages over mechanically registered compounding methods previously employed in the breast and significant increases in lesion and structural conspicuity are noted due to a reduction in speckle noise. The improvements from compounding in 3D, surface-rendered Doppler imaging of vasculature are striking.

Adenocarcinoma↗

Simulation of mode-locked surface-emitting lasers through a finite-difference time-domain algorithm.

An approach based on the finite-difference time-domain method is developed for simulating the dynamics of passive mode locking in vertical-cavity surface-emitting lasers (VCSELs). The material response is modeled by the effective semiconductor Bloch equations through a resonant polarization term in the Maxwell's equations. Nonlinear gain saturation is incorporated through a gain compression factor in the equation governing the dynamics of the resonant polarization. An extended-cavity VCSEL with a quantum-well saturable absorber is simulated, and stable mode-locking pulses are obtained. Fine features of the spatial profile of the mode-locked pulses are also studied within this approach.

Journal Article↗