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Sources of variation in Affymetrix microarray experiments

BMC BIOINFORMATICS 2005年第1期6卷 214-214页

作者： Zakharkin, SO Kim, K Mehta, T Chen, L Barnes, S Scheirer, KE Parrish, RS Allison, DB Page, GP Univ Alabama Birmingham Sect Stat Genet Birmingham AL 35294 USA Univ Alabama Birmingham Dept Pharmacol Birmingham AL 35294 USA Univ Alabama Birmingham Dept Toxicol Birmingham AL 35294 USA Univ Alabama Birmingham Heflin Ctr Human Genet Birmingham AL 35294 USA Univ Louisville Dept Bioinformat & Biostat Louisville KY 40292 USA

Background: A typical microarray experiment has many sources of variation which can be attributed to biological and technical causes. Identifying sources of variation and assessing their magnitude, among other factors, are important for optimal experimental design. The objectives of this study were: (1) to estimate relative magnitudes of different sources of variation and (2) to evaluate agreement between biological and technical replicates. Results: We performed a microarray experiment using a total of 24 Affymetrix GeneChip (R) arrays. The study included 4th mammary gland samples from eight 21-day-old Sprague Dawley CD female rats exposed to genistein (soy isoflavone). RNA samples from each rat were split to assess variation arising at labeling and hybridization steps. A general linear model was used to estimate variance components. Pearson correlations were computed to evaluate agreement between technical and biological replicates. Conclusion: The greatest source of variation was biological variation, followed by residual error, and finally variation due to labeling when *.cel files were processed with dChip and RMA image processing algorithms. When MAS 5.0 or GCRMA-EB were used, the greatest source of variation was residual error, followed by biology and labeling. Correlations between technical replicates were consistently higher than between biological replicates.

关键词： Genistein Residual Error Microarray Experiment Affymetrix GeneChip image processing algorithm

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Blinking supervision in a working environment

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JOURNAL OF BIOMEDICAL OPTICS 2016年第2期21卷 025005-025005页

作者： Morcego, Bernardo Argiles, Marc Cabrerizo, Marc Cardona, Genis Perez, Ramon Perez-Cabre, Elisabet Gispets, Joan Univ Politecn Cataluna Adv Control Syst Res Grp Rambla Sant Nebridi 10 Terrassa 08222 Spain Univ Politecn Cataluna Dept Opt & Optometry Sch Opt & Optometry C Violinista Vellsola 37 Terrassa 08222 Spain

The health of the ocular surface requires blinks of the eye to be frequent in order to provide moisture and to renew the tear film. However, blinking frequency has been shown to decrease in certain conditions such as when subjects are conducting tasks with high cognitive and visual demands. These conditions are becoming more common as people work or spend their leisure time in front of video display terminals. Supervision of blinking frequency in such environments is possible, thanks to the availability of computer-integrated cameras. Therefore, the aim of the present study is to develop an algorithm for the detection of eye blinks and to test it, in a number of videos captured, while subjects are conducting a variety of tasks in front of the computer. The sensitivity of the algorithm for blink detection was found to be of 87.54% (range 30% to 100%), with a mean false-positive rate of 0.19% (range 0% to 1.7%), depending on the illumination conditions during which the image was captured and other computer-user spatial configurations. The current automatic process is based on a partly modified pre-existing eye detection and image processing algorithms and consists of four stages that are aimed at eye detection, eye tracking, iris detection and segmentation, and iris height/width ratio assessment. (C) 2016 Society of Photo-Optical Instrumentation Engineers (SPIE)

关键词： automatic eye blink detection blinking frequency image processing algorithm computer vision syndrome video display terminal dry eye webcam

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Assessment of black rot development on apple surface using laser biospeckle technique

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PHYSICA SCRIPTA 2023年第3期98卷 035501-035501页

作者： Koley, Chhanda Das, Rittik Nirala, Anil Kumar Indian Inst Technol Indian Sch Mines Dhanbad Dept Phys Biomed Opt Lab Dhanbad Jharkhand India

In our present study, the laser biospeckle technique has been applied to monitor the spread of black rot fungal disease and evaluate the infected area on apple surface for the first time to the best of our knowledge. image processing algorithms such as inertia moment (IM), absolute value of differences (AVD) and spatial-temporal speckle correlation show the reduction of biospeckle activity of the black rot infected apples in comparison to that of the healthy apples with increase in time, once the visible symptom of the disease sets in. Spectral activity maps obtained using Fujii, inverse Fujii and parameterized Fujii show the spread of this infection with the progression of day. Under exposition test and histogram plot have been used to evaluate the increase of darkness of the infected apple with the progression of day and the results have come out as a replica of the change of colour of the region of interest. % biospeckle activity loss on the final day of the experiment has been found to be 17.83% and 11.91% for healthy apples & 92.42% and 78.63% for infected apples using IM and AVD respectively. An increase in the infected area and % increase in infected area of the region of interest on the image plane has been determined to be 0.33 mm(2) and 58.57% respectively on the final day of the experiment.

关键词： biospeckle image processing algorithm black rot disease apple

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Improvement of video playback performance of electrophoretic displays by optimized waveforms with shortened refresh time

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Displays 2017年 49卷 95-100页

作者： Li Wang Zichuan Yi Mingliang Jin Lingling Shui Guofu Zhou Institute of Electronic Paper Displays Academy of South China Advanced Optoelectronics South China Normal University Guangzhou 510006 China Academy of Shenzhen Guohua Optoelectronics Shenzhen 518110 China University of Electronic Science and Technology of China Zhongshan Institute School of Electronic and Information Engineering Zhongshan 528402 China

Electrophoretic display (EPD) has become one of the most important display technologies due to its bistability, low power consumption and outdoor readability. In this work, an image processing algorithm, which aims to enable video playback on EPD device without image distortion and grayscale loss by reducing the particle moving distance in EPD, is proposed and verified. The refresh time could be shortened by 22.2% with a video playback speed of more than 10 frames per second (fps) being achieved. This method could reduce the EPD switching time for quicker information displaying, and potentially extend the applications of EPD with video-like display property in the future.

关键词： Electrophoretic display image processing algorithm Video playback image distortion Refresh time

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Alveolar morphology depends on ventilator settings: lessons from in vivo alveolar microscopy under static and dynamic conditions

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Crit Care 2011年第SUPPL 1期15卷 P178-P178页

作者： D Schwenninger S Schumann J Guttmann University Medical Center Freiburg Germany

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Application of digital holographic microscopy to evaluate the dynamics of a single red blood cell influenced by low-power laser light

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OPTICS AND LASER TECHNOLOGY 2021年 142卷 107262-107262页

作者： Kucharski, Dawid Bartczak, Monika Poznan Univ Tech Inst Mech Technol Div Metrol & Measurement Syst Poznan Poland

In the paper, a shift of individual human erythrocytes drifts speed, stimulated by various low-power lasers irradiation, was studied by digital holographic microscopy (DHM). Well known in physiotherapy, a low-levellaser-therapy (LLLT) scanner was used as the stimulation light source, with diode and He-Ne lasers to compare. In the article, an open-source image processing algorithm for simultaneous dynamics and geometrical properties evaluations of the red blood cells is proposed. A strong influence of the low-level red light on the red blood cells dynamics was observed. The effect is important for a better understanding of the laser treatment mechanism. The proposed phase image analysis algorithm significantly improves the individual cells tracing precision for a life science application. The programme might be useful for optical tweezer, imaging flow cytometry, or high precision cells-photon interaction research.

关键词： Digital holographic microscopy Optical tweezers Optical metrology image processing algorithm Red blood cells R programming

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Compensating over- and underexposure in optical target pose determination

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PATTERN RECOGNITION 2021年 116卷 107930-107930页

作者： Cledat, E. Rufener, M. Cucci, D. A. EPFL ENAC TOPO Batiment GC Stn 18 CH-1015 Lausanne Switzerland

Optical coded targets allow to determine the relative pose of a camera, on a metric scale, from one image only. Furthermore, they are easily and efficiently detected, opening to a wide range of applications in robotics and computer vision. In this work we describe the effect of pixel saturation and non-ideal lens Point Spread Function, causing the apparent position of the corners and the edges of the target to change as a function of the camera exposure time. This effect, which we call exposure bias, is frequent in over or underexposed images and introduces a systematic error in the estimated camera pose. We propose an algorithm that is able to estimate and correct for the exposure bias exploiting specific geometric features of a common target design based on concentric circles. Through rigorous laboratory experiments carried out in a highly controlled environment, we demonstrate that the proposed algorithm is seven times more precise and three times more accurate in the target distance estimation than the algorithms available in the literature. (c) 2021 Elsevier Ltd. All rights reserved.

关键词： Optical target Target orientation image processing algorithm Geometry Ellipse fitting Computer vision Overexposure Exposure compensation Resection

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A Two-Stage Approach to Important Area Detection in Gathering Place Using a Novel Multi-Input Attention Network

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SENSORS 2022年第1期22卷 285-285页

作者： Xu, Jianqiang Zhao, Haoyu Min, Weidong Nanchang Univ Sch Informat Engn Nanchang 330031 Jiangxi Peoples R China Nanchang Univ Sch Software Nanchang 330047 Jiangxi Peoples R China Jiangxi Key Lab Smart City Nanchang 330047 Jiangxi Peoples R China

An important area in a gathering place is a region attracting the constant attention of people and has evident visual features, such as a flexible stage or an open-air show. Finding such areas can help security supervisors locate the abnormal regions automatically. The existing related methods lack an efficient means to find important area candidates from a scene and have failed to judge whether or not a candidate attracts people's attention. To realize the detection of an important area, this study proposes a two-stage method with a novel multi-input attention network (MAN). The first stage, called important area candidate generation, aims to generate candidate important areas with an image-processing algorithm (i.e., K-means++, image dilation, median filtering, and the RLSA algorithm). The candidate areas can be selected automatically for further analysis. The second stage, called important area candidate classification, aims to detect an important area from candidates with MAN. In particular, MAN is designed as a multi-input network structure, which fuses global and local image features to judge whether or not an area attracts people's attention. To enhance the representation of candidate areas, two modules (i.e., channel attention and spatial attention modules) are proposed on the basis of the attention mechanism. These modules are mainly based on multi-layer perceptron and pooling operation to reconstruct the image feature and provide considerably efficient representation. This study also contributes to a new dataset called gathering place important area detection for testing the proposed two-stage method. Lastly, experimental results show that the proposed method has good performance and can correctly detect an important area.

关键词： important area detection image processing algorithm multi-input attention network gathering place important area detection dataset

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Kinect Evaluation for Human Body Movement Analysis

Kinect Evaluation for Human Body Movement Analysis

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IEEE RAS & EMBS International Conference on Biomedical Robotics and Biomechatronics

作者： Leonardo Marquez Pedro Glauco Augusto de Paula Caurin Mechatronics Laboratory Engineering School of Sao Carlos University of Sao Paulo

ISBN: (纸本)9781457711992

The movement analysis of the human body is an interesting task for applications in rehabilitation assisted by robots and robotic manipulation. This paper presents a simplified system using the Kinect sensor and simple image processing algorithms for the extraction of identification points. Experiments were conducted to identify whether the sensor has good characteristics for the considered applications. A repeatability experiment were carried out and its results indicate that the sensor can be used to measure three-dimensional identification points distances regarding the applications requirements within the operational range from 0.5m up to 2m.

关键词： Human Body game player Sensors operating range Robot image processing algorithm Rehabilitation

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High-Sensitive and High-Efficient Biochemical Analysis Method Using a Bionic Electronic Eye in Combination with a Smartphone-based Colorimetric Reader System

High-Sensitive and High-Efficient Biochemical Analysis Metho...

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Annual International Conference of the IEEE Engineering in Medicine and Biology Society

作者： Kaiqi Su Quchao Zou Ning Hu Ping Wang Dept. of Biomed. Eng. Zhejiang Univ. Hangzhou China

ISBN: (纸本)9781424492695

Bionic electronic eye (Bionic e-Eye), a developed smartphone-based colorimetric reader system, consists of smartphone or pad (iPhone 4s or iPad 3) as detection instrument and portable accessory as illumination provider, integrating with a wide-angle lens, a piece of lowest-power electro luminescent and a custom-made dark hood. A 96-well microtiter plate (MTP) was positioned on the electro luminescent and Bionic e-Eye captures the detection images by the back camera of smartphone. Being similar to human visual system, the hue, saturation and value (HSV, also called hex cone model) color model was employed in image processing algorithm of Bionic e-Eye. Optimized system dimension was determined by the system steadiness experiment of different photograph distances. Moreover, the commercially available BCA protein assay and CCK8 cell number assay were carried out to evaluate this Bionic e-Eye. Analytical performance of Bionic e-Eye had the better precision, higher sensitivity than microtiter plate reader (MTPR) and previous smartphone-based colorimetric reader for both two assays. Also, Bionic e-Eye using optical image detection had simultaneous and synchronous working mode, while MPTR using machine moving detection had asynchronous working mode in high throughput detection. Therefore, Bionic e-Eye will be an ideal point-of-care (POC) colorimetric detection device in the field of clinical application, industrial quality control, environment monitoring, and food assessment.

关键词： biochemistry biomedical electronics biomedical optical imaging cellular biophysics colorimetry electroluminescent devices proteins smart phones BCA protein assay Bionic e-Eye CCK8 cell number assay bionic electronic eye clinical application color model colorimetric detection device custom-made dark hood detection image detection instrument environment monitoring food assessment hex cone model high-efficient biochemical analysis method high-sensitive biochemical analysis method human visual system image processing algorithm industrial quality control lowest-power electroluminescent microtiter plate reader optical image detection optimized system dimension portable accessory smartphone camera smartphone-based colorimetric reader system Biological system modeling Biomedical imaging image color analysis Lenses Proteins Sensitivity Tablet computers Smartphone bionics industrial quality control image processing algorithm Tablet Computers COLOR MODEL environmental monitoring Biological system modeling image colour analysis cellular biophysics Biomedical optical imaging Biomedical imaging protein determination Electroluminescent devices colorimetry

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