KEYWORDS: Control systems, Temperature metrology, Human-machine interfaces, Fluctuations and noise, Control systems design, Analytical research, Computing systems, Process control, Telecommunications, Computer architecture
Effective host-local system architecture for PCR chips is presented. The functions required for the control of the chips
and their partitioning into the host and the local system are qualitatively analyzed. The results indicated that, most
functions can be resided in the host to deliver the benefits on the development period, the system cost, and the
maintenance. The control system was implemented with PC as the host and the local system was connected by USB
interface, obtaining the superior development and the GUI design environment. A PCB-based PCR chip example was
constructed and tested to verify the proposed system.
Template matching method is presented to identify the peaks from the scanned signals of lateral flow immunoassay
strips. The template is composed of two pulses separated by the distance of the control and the target ligand line in the
assay, and is convolved with the scanned signal to deliver the maximum at the center of the two peaks. The peak regions
were identified with the predefined distances from the center. Glycosylated haemoglobin immunoassay strips and
fluorescent strip readers from Boditechmed Inc. were tested to estimate the lot and reader variations of the concentration
measurands. The results showed the robustness of the propose method.
We propose a nonlinear matching measure, called counting measure, as a signal detection measure that is defined as the number of on pixels in the spot area. It is applied to classify probes for an on-off type DNA microarray, where each probe spot is classified as hybridized or not. The counting measure also incorporates the maximum response search method, where the expected signal is obtained by taking the maximum among the measured responses of the various positions and sizes of the spot template. The counting measure was compared to existing signal detection measures such as the normalized covariance and the median for 2390 patient samples tested on the human papillomavirus (HPV) DNA chip. The counting measure performed the best regardless of whether or not the maximum response search method was used. The experimental results showed that the counting measure combined with the positional search was the most preferable.
We propose a new nonlinear matching measure for automatic analysis of the on-off type DNA microarray images in which the hybridized spots are detected by a template-matching method. The proposed measure is obtained by binary thresholding over the entire template region and taking the number of white pixels inside the spotted area. This measure is compared with the normalized covariance method in terms of classifying the ability to successfully locate markers. The proposed measure was evaluated for scanned images of human papillomavirus (HPV) DNA microarrays where locating markers is a critical issue because of the small number of spots. The targeting spots of HPV DNA chips are designed for genotyping twenty-two types of the human papillomavirus. The proposed measure is proven to give a more discriminative response, reducing the missed cases of successful marker location. The locating accuracy of the proposed method is also shown to have the same performance as that of the normalized covariance.
In this paper, we propose a new nonlinear matching measure for automatic analysis of the on-off type DNA microarray images in which the hybridized spots are detected by the template matching method. The targeting spots of HPV DNA chips are designed for genotyping the human papilloma virus(HPV). The proposed measure is obtained by binarythresholding over the whole template region and taking the number of white pixels inside the spotted area. This measure
is evaluated in terms of the accuracy of the estimated marker location to show better performance than the normalized covariance.
This paper addresses the image processing technique for discriminating whether the probes are hybrized with target DNA in the Human Papilloma Virus (HPV) DNA Chip designed for genotyping HPV. In addition to the probes, the HPV DNA chip has markers that always react with the sample DNA. The positions of probe-dots in the final scanned image are fixed relative to the marker-dot locations with a small variation according to the accuracy of the dotter and the scanner. The probes are duplicated 4 times for the diagnostic stability. The prior knowledges such as the maker relative distance and the duplication information of probes is integrated into the template matching technique with the normalized correlation measure. Results show that the employment of both of the prior knowledges is to simply average the template matching measures over the positions of the markers and probes. The eventual proposed scheme yields stable marker locating and probe classification.
As medical imaging is adapting to the digital technology, solid imaging sensors are replacing the classical films in dental application. CCD is one of the typical image senors in this are. In the oral imaging, however, the size of image sensors should be large because there is not enough space for optical path of lens inside the mouth. The unavoidable defects are usually occurred in the large format CCD sensor. Practically it is not possible to get the defect free sensor because its cost is rapidly increasing to reduce the defects. In this paper we will present an efficient strategy to handle these defects. As the lighting is highly controllable differently from the common cameras, the controlled illumination is used to create uniform images with various levels. The local statistics in each controlled image are investigated to find defected areas. All the defected regions of each image are accumulated forming image-like representation. The defected regions are concealed with their neighbors by linear interpolation.
In this paper the design considerations for a digital dental x-ray system is discussed where a commercial CCD sensor is adopted. Especially the system should be able to work with several x-ray machines even with them for the classical film. The hardware-software co-design methodology is employed to optimize the system. The full digital implementation is assumed for the reliability of the system. The considered functions cover the pre-processing such as the exposure detection, clamping and the dark level correction and the post-processing such as gray level compensation. It is analyzed with some other constraints in order to make the final partition. The entire system based on the partition will be described.
While the DNA chip is going to be prevalent for the medical diagnostics and drug development, its analysis tool such as a chip scanner need to be optimized. To obtain the guideline for the optimized CCD-based scanner, this paper addresses the minimum requirements for the selected CCD-based detector under the chosen light condition. The scope of our experiments was focused on the scanning performance rather than the design of the chip scanner itself. Through the gray level analysis of the target spot and background, we could check the possibility of the CCD-based detector and the lighting lamp to adopt them as a low price scanner. A quality measure was investigated with two levels of lighting power and the various integration times. For the CCD-based detector and the Xenon lighting system, we evaluated the image performance with the developed quality measure. We define a background and a sample area mask manually to investigate the statistics of the images captured by the scanner. The developed system is composed with a medium price CCD camera and a zenon lamp lighting system. The developed system has reasonable performance for the scanned image. The risk ofphotobleaching was not shown in our experiments.
The importance and effects of data preprocessing and wavelength selection were investigated in predicting total hemoglobin concentrations form absorption spectra. Spectra of the 1 nm interval between 500-900nm were measured from the whole blood samples taken form 165 patients whose hemoglobin concentrations ranged between 7-17 g/dl. The concentrations were predicted using the partial least squares regression. A total of 18 different combinations of preprocessing were tested. The partial least squares regression analysis provided quite different results depending on preprocessing methods and a wide range of prediction accuracy was obtained. For example, the sum of squares of difference ranged from 6-18.6, R2 varied from 0.8333 to 0.9477 and the root mean squared errors were from 0.5504-0.966 g/dl. The best results was obtained from the data processed by linear regression baseline fitting, unit area correction, mean centering and variance scaling. Instead of using all wavelengths in the broad-band spectra, a discrete number of wavelengths were selected to predict the concentrations using our algorithm, which will be advantageous in developing compact and less expensive commercial devices. It proves that a careful selection of wavelengths can provide a comparable accuracy obtained from using the broad-band spectra. For our particular experimental data, the measurement form only three discrete wavelengths could provide excellent results.
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