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PubMedDate not supplied

On lossy transform compression of ECG signals with reference to deformation of their parameter values.

Electrocardiogram (ECG) signals are the most prominent biomedical signal type used in clinical medicine. Their compression is important and widely researched in the medical informatics community. In the previous literature compression efficacy has been investigated only in the context of how much known or developed methods reduced the storage required by compressed forms of original ECG signals. Sometimes statistical signal evaluations based on, for example, root mean square error were studied. In previous research we developed a refined method for signal compression and tested it jointly with several known techniques for other biomedical signals. Our method of so-called successive approximation quantization used with wavelets was one of the most successful in those tests. In this paper, we studied to what extent these lossy compression methods altered values of medical parameters (medical information) computed from signals. Since the methods are lossy, some information is lost due to the compression when a high enough compression ratio is reached. We found that ECG signals sampled at 400 Hz could be compressed to one fourth of their original storage space, but the values of their medical parameters changed less than 5% due to compression, which indicates reliable results.

Algorithms↗
PubMed2006

On the use of standards for microarray lossless image compression.

The interest in methods that are able to efficiently compress microarray images is relatively new. This is not surprising, since the appearance and fast growth of the technology responsible for producing these images is also quite recent. In this paper, we present a set of compression results obtained with 49 publicly available images, using three image coding standards: lossless JPEG2000, JBIG, and JPEG-LS. We concluded that the compression technology behind JBIG seems to be the one that offers the best combination of compression efficiency and flexibility for microarray image compression.

Data Compression↗
PubMed2005

Optimization of integer wavelet transforms based on difference correlation structures.

In this paper, a novel lifting integer wavelet transform based on difference correlation structure (DCCS-LIWT) is proposed. First, we establish a relationship between the performance of a linear predictor and the difference correlations of an image. The obtained results provide a theoretical foundation for the following construction of the optimal lifting filters. Then, the optimal prediction lifting coefficients in the sense of least-square prediction error are derived. DCCS-LIWT puts heavy emphasis on image inherent dependence. A distinct feature of this method is the use of the variance-normalized autocorrelation function of the difference image to construct a linear predictor and adapt the predictor to varying image sources. The proposed scheme also allows respective calculations of the lifting filters for the horizontal and vertical orientations. Experimental evaluation shows that the proposed method produces better results than the other well-known integer transforms for the lossless image compression.

Algorithms↗
PubMed2004

Compressed pattern matching in DNA sequences.

We propose derivative Boyer-Moore (d-BM), a new compressed pattern matching algorithm in DNA sequences. This algorithm is based on the Boyer-Moore method, which is one of the most popular string matching algorithms. In this approach, we compress both DNA sequences and patterns by using two bits to represent each A, T, C, G character. Experiments indicate that this compressed pattern matching algorithm searches long DNA patterns (length > 50) more than 10 times faster than the exact match routine of the software package Agrep, which is known as the fastest pattern matching tool. Moreover, compression of DNA sequences by this method gives a guaranteed space saving of 75%. In part the enhanced speed of the algorithm is due to the increased efficiency of the Boyer-Moore method resulting from an increase in alphabet size from 4 to 256.

Algorithms↗
PubMed1997

Wavelet transform-based image compression for transmission of MR data.

OBJECTIVE: The purpose of this study was to develop an effective, inexpensive teleradiology image-transmission system for transfer of MR studies using wavelet transform image compression. CONCLUSION: We describe an efficient system for implementing teleradiology capability for transmission of diagnostic MR images. The system uses the wavelet transform to achieve greater than 90% image compression, with standard modern transmission times of less than 5 sec per compressed image. The method is inexpensive and can be implemented using commonly available workstation and MR scanner capabilities.

Brain↗
PubMed2004

Initial study of honey adulteration by sugar solutions using midinfrared (MIR) spectroscopy and chemometrics.

Fourier transform infrared (FTIR) spectroscopy and attenuated total reflection (ATR) sampling have been used to detect adulteration of honey samples. The sample set comprised 320 spectra of authentic (n = 99) and adulterated (n = 221) honeys. Adulterants used were solutions containing both d-fructose and d-glucose prepared in the following respective weight ratios: 0.7:1.0, 1.2:1.0 (typical of honey composition), and 2.3:1.0. Each adulterant solution was added to individual honeys at levels of 7, 14, and 21% w/w. Spectral data were compressed and analyzed using k-nearest neighbors (kNN) and partial least squares (PLS) regression techniques. A number of data pretreatments were explored. Best classification models were achieved with PLS regression on first derivative spectra giving an overall correct classification rate of 93%, with 99% of samples adulterated at levels of 14% w/w or greater correctly identified. This method shows promise as a rapid screening technique for detection of this type of honey adulteration.

Carbohydrates↗
PubMed2000

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↗
PubMed2006

Neuronal loss and expression of neurotrophic factors in a model of rat chronic compressive spinal cord injury.

STUDY DESIGN: An experimental animal study about neuronal loss and the expression of neurotrophic factors in the chronic compressive spinal cords. OBJECTIVES: To investigate neuronal loss and the expression of neurotrophic factors in the chronic compressive spinal cords of rats, and to evaluate effects of decompressive procedures for the neuronal loss. SUMMARY OF BACKGROUND DATA: Chronic compression of spinal cords induces the loss of motor neurons in the anterior horn. However, the precise mechanism of this neuronal loss is not still understood completely. Furthermore, it is uncertain whether decompressive procedures prevent this neuronal loss or not. METHODS: A thin expanding polymer sheet was implanted microsurgically underneath T7 laminae of rats. After 6, 9, 12, and 15 weeks, the thoracic spinal cord was harvested and examined histopathologically. The expression of neurotrophic factors, including NGF, BDNF, NT-3, GDNF, CNTF, and VEGF, was analyzed using semiquantitative RT-PCR, enzyme immunoassay, and immunohistochemistry. Decompressive surgery was performed through the removal of T7 laminae and the compression materials 6, 9, and 12 weeks after starting compression. Three weeks later, respectively, the neuronal loss in the anterior horn was estimated. RESULTS: The spinal cords were progressively flattened by the expanding of the implanted polymer sheet, and the number of motor neurons in the anterior horn decreased, especially from 6 to 9 weeks after starting compression. Semiquantitative RT-PCR analysis showed that the expression of NGF and BDNF mRNAs was decreased significantly in the spinal cords of 12-week compression group compared with the 6-week compression group and that NGF mRNA expression was up-regulated significantly in the 6-week compression group relative to the 6-week control group. Any changes of expression of other neurotrophic factors were not significant. Since BDNF, not NGF, has been known to be one of the powerful survival factors for spinal motoneurons, we investigated the levels of BDNF protein in the compressive spinal cords using enzyme immunoassay and immunohistochemistry. We demonstrated the level of BDNF protein in the compressive spinal cords was increased 6 weeks after compression but declined after 12 weeks. The decompressive procedure in the 6 weeks after compression prevented neuronal loss, but the same procedure in the 9 or 12 weeks was ineffective. CONCLUSIONS: From the point of view of neuronal loss, decompressive surgery at an earlier stage, when compensatory mechanisms including the up-regulation of BDNF might be still effective, could provide better therapeutic results against chronic mechanical compressive spinal cord lesions.

Animals↗
PubMed2005

Mutual information-based analysis of JPEG2000 contexts.

Context-based arithmetic coding has been widely adopted in image and video compression and is a key component of the new JPEG2000 image compression standard. In this paper, the contexts used in JPEG2000 are analyzed using the mutual information, which is closely related to the compression performance. We first show that, when combining the contexts, the mutual information between the contexts and the encoded data will decrease unless the conditional probability distributions of the combined contexts are the same. Given I, the initial number of contexts, and F, the final desired number of contexts, there are S(I, F) possible context classification schemes where S(I, F) is called the Stirling number of the second kind. The optimal classification scheme is the one that gives the maximum mutual information. Instead of using an exhaustive search, the optimal classification scheme can be obtained through a modified generalized Lloyd algorithm with the relative entropy as the distortion metric. For binary arithmetic coding, the search complexity can be reduced by using dynamic programming. Our experimental results show that the JPEG2000 contexts capture the correlations among the wavelet coefficients very well. At the same time, the number of contexts used as part of the standard can be reduced without loss in the coding performance.

Algorithms↗
PubMed1991

Trends in future urodynamics: computer support-data base-digitized imaging.

The use of computers in urodynamics must be based preferably on the structure of the urodynamic investigation itself. This enables implementation of computerized systems in the urodynamic laboratory in the most natural way and provides transparency of urodynamic software for the investigators. Additionally, the algorithms of the urodynamic software then can provide for a urodynamic investigation following a logical path based on the patient's history and clinical data and (automatically interpreted) results from earlier steps in the urodynamics. As an extension of this structured logical reasoning, the computer use in urodynamics can be extended to include validation and decision rules, comprising measurement data and rules for interpretation and combination of history, clinical and measurement data. Conclusions will be presented then in the form of a preliminary differential diagnosis, including the odds for each of the possible diagnoses. These kinds of computerized interpretation systems will be validated by comparison with the classical clinical diagnoses and are generally known as expert systems. These systems rely on logical branching-as opposed to systems that are statistical in nature and use large data bases to classify individual data into known groups. Data bases will remain for the purpose of documentation, based on individual patients and comprising all patient data-comparable to the existing patient files in the hospital's archives. The computer files have to include also the original data from functional studies like urodynamics-and not just the abstracted conclusions-and from imaging techniques. Intelligent compression of data prevents the data bases from exploding. Digital imaging techniques combined with computerized urodynamic investigations open possibilities for dynamic analysis of morphologic data and combination thereof with urodynamic measurement data.

Databases, Factual↗