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2006 IEEE/NLM Life Science Systems and Applications Workshop最新文献

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Examining Phenotype Differences in Mouse Placenta with Volume Rendering and Segmentation 用体积绘制和分割技术研究小鼠胎盘的表型差异
2006 IEEE/NLM Life Science Systems and Applications Workshop Pub Date : 2006-11-30 DOI: 10.1109/LSSA.2006.250431
R. Sharp, R. Ridgway, K. Mosaliganti, O. Irfanoglu, P. Wenzel, R. Machiraju, A. de Bruin, G. Leone, T. Pan, Kun Huang, J. Saltz
{"title":"Examining Phenotype Differences in Mouse Placenta with Volume Rendering and Segmentation","authors":"R. Sharp, R. Ridgway, K. Mosaliganti, O. Irfanoglu, P. Wenzel, R. Machiraju, A. de Bruin, G. Leone, T. Pan, Kun Huang, J. Saltz","doi":"10.1109/LSSA.2006.250431","DOIUrl":"https://doi.org/10.1109/LSSA.2006.250431","url":null,"abstract":"We present an application problem of examining phenotype differences in wildtype and retinoblastoma (Rb) knockout specimens of mouse placenta. The lack of the Rb gene causes uncontrolled tissue growth which forces infiltrations into critical sections of mouse placenta that lead to fetal death. We briefly describe our method for volume visualization of mouse placenta tissue level intermixing at a microscopic scale for both wildtype and Rb knockout types. Our technique combines non-trivial registration techniques, an TV-point correlation classifier, and a volume rendering step. Our final volume renderings show tissue intermixing differences between both wildtype and Rb knockout specimens that are not obvious from examining the two dimensional image stack alone","PeriodicalId":360097,"journal":{"name":"2006 IEEE/NLM Life Science Systems and Applications Workshop","volume":"13 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2006-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125167221","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
High-Degree Concentration of Bio-agents using Electrokinetic Manipulations 利用电动操作高浓度生物制剂
2006 IEEE/NLM Life Science Systems and Applications Workshop Pub Date : 2006-11-30 DOI: 10.1109/LSSA.2006.250373
K. Murray, Tza-Huei Wang, K. Rebello, J. Crookston, J. Miragliotta
{"title":"High-Degree Concentration of Bio-agents using Electrokinetic Manipulations","authors":"K. Murray, Tza-Huei Wang, K. Rebello, J. Crookston, J. Miragliotta","doi":"10.1109/LSSA.2006.250373","DOIUrl":"https://doi.org/10.1109/LSSA.2006.250373","url":null,"abstract":"Techniques used for the upstream collection of bio-warfare agents often result in a large, dilute sample volume composed of a wide variety of moieties. Nonetheless, current bioassays, though constantly being refined, benefit from a highly concentrated sample, leading to an enhanced signal to noise ratio and increasing the ultimate sensitivity. This report describes an electrokinetics-based sample concentration device designed to concentrate bio-agents, such as bacillus spores, from a relatively large volume (~500 mul) to be within a nanoliter volume for downstream target processing and detection. The concentrator can later be integrated with other fluidic sample processing devices and sensors for the development of a stand-alone bio-agent surveillance system","PeriodicalId":360097,"journal":{"name":"2006 IEEE/NLM Life Science Systems and Applications Workshop","volume":"21 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2006-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130108699","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Turbo Data Integration for Uncovering Gene Networks 揭示基因网络的Turbo数据集成
2006 IEEE/NLM Life Science Systems and Applications Workshop Pub Date : 2006-11-30 DOI: 10.1109/LSSA.2006.250397
Yufei Huang, Yufang Yin
{"title":"Turbo Data Integration for Uncovering Gene Networks","authors":"Yufei Huang, Yufang Yin","doi":"10.1109/LSSA.2006.250397","DOIUrl":"https://doi.org/10.1109/LSSA.2006.250397","url":null,"abstract":"Data integration is an important task in the gene network research. In this paper, the integration of two microarray datasets for uncovering gene networks is considered. The premise of data integration is that different datasets all carry information about the common networks of interest. Thus, through data fusion, the authors hope to combine information from different sources to gain improved understanding about the networks. Inspired by the similarity between the data integration problem and turbo decoding in wireless communications, a Bayesian data integration framework based on a turbo approach was proposed. The proposed algorithm was tested on two microarray datasets of 10 genes in the yeast cell cycle","PeriodicalId":360097,"journal":{"name":"2006 IEEE/NLM Life Science Systems and Applications Workshop","volume":"59 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2006-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"133245062","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Microwave Dielectric Properties of On-Chip Liquid Films 片上液体薄膜的微波介电特性
2006 IEEE/NLM Life Science Systems and Applications Workshop Pub Date : 2006-11-30 DOI: 10.1109/LSSA.2006.250401
C. Song, S. Azimuudin, Byungje Lee, F. Harackiewicz, M. Yen, D. Ralu, A. Hoffman, Pingshan Wang
{"title":"Microwave Dielectric Properties of On-Chip Liquid Films","authors":"C. Song, S. Azimuudin, Byungje Lee, F. Harackiewicz, M. Yen, D. Ralu, A. Hoffman, Pingshan Wang","doi":"10.1109/LSSA.2006.250401","DOIUrl":"https://doi.org/10.1109/LSSA.2006.250401","url":null,"abstract":"A microwave characterization method for on-chip liquid film dielectric property measurement is developed. Microstrip-line based on-chip test structures are fabricated to characterize the microwave dielectric properties of various on-chip liquid films: DI water and binary mixtures of DI water with glucose and ethanol. The obtained microwave dielectric properties are presented in Cole-Cole diagrams, which show general frequency dependence similar to that of bulk liquids. Different concentration levels of glucose and ethanol show different microwave dielectric responses. Therefore, on-chip microwave dielectric spectroscopy provides a promising and inexpensive on-chip sensing mechanism for biomedical and chemical applications","PeriodicalId":360097,"journal":{"name":"2006 IEEE/NLM Life Science Systems and Applications Workshop","volume":"15 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2006-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131902461","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Integrated PDMS/CMOS Microsystem for Autonomous Incubation and Imaging in Cell Culture Studies 集成PDMS/CMOS微系统在细胞培养研究中的自主孵化和成像
2006 IEEE/NLM Life Science Systems and Applications Workshop Pub Date : 2006-11-30 DOI: 10.1109/LSSA.2006.250430
J.M. Blain Christen, A. Andreou
{"title":"Integrated PDMS/CMOS Microsystem for Autonomous Incubation and Imaging in Cell Culture Studies","authors":"J.M. Blain Christen, A. Andreou","doi":"10.1109/LSSA.2006.250430","DOIUrl":"https://doi.org/10.1109/LSSA.2006.250430","url":null,"abstract":"We discuss the design, fabrication and testing of a hybrid microsystem for stand-alone cell culture, incubation and imaging. The micro-incubator is engineered through the integration of two CMOS dies. The first for the heater and temperature sensor, and a second die for imaging. A multilayer PDMS (polydimethylsiloxane) structures is used to create not only the fluidic structures but to encapsulate the CMOS dies. The microfluidic features include fluidic channels, a 4 mm diameter, 30muL, culture well and a 25 micron thick PDMS membrane that covers the top of the culture well, acting as barrier to contaminants while allowing the cells to exchange gases with the ambient environment. The micro-incubator interface includes with a flexible polyimide ribbon cable and four fluidic ports. The complete structure has a size of (2.5times2.5times0.6 cm3). We have employed the device to successfully culture BHK-21 cells autonomously over a sixty hour period in ambient environment","PeriodicalId":360097,"journal":{"name":"2006 IEEE/NLM Life Science Systems and Applications Workshop","volume":"456 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2006-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116169906","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 4
Classify cellular phenotype in high-throughput fluorescence microcopy images for RNAi genome-wide screening 在RNAi全基因组筛选的高通量荧光显微图像中分类细胞表型
2006 IEEE/NLM Life Science Systems and Applications Workshop Pub Date : 2006-11-30 DOI: 10.1109/LSSA.2006.250404
Jun Wang, Xiaobo Zhou, Fuhai Li, Stephen T. C. Wong
{"title":"Classify cellular phenotype in high-throughput fluorescence microcopy images for RNAi genome-wide screening","authors":"Jun Wang, Xiaobo Zhou, Fuhai Li, Stephen T. C. Wong","doi":"10.1109/LSSA.2006.250404","DOIUrl":"https://doi.org/10.1109/LSSA.2006.250404","url":null,"abstract":"As we know, the genes could cause the cell phenotypes to change dramatically. Currently, biologists attempt to perform the genome-wide RNAi screening to identify various image phenotypes. It is a challenging task to recognize the phenotypes automatically because of the noisy background and low contrast of fluorescence images. In this work, we applied two cellular segmentation techniques, deformable model and Cellprofiler software, for the preprocess of cellular segmentation. Then five kinds of features including wavelet feature, moments feature, haralick co-occurrence feature, region property feature, and problem-specific shape descriptor are extracted from the cellular patches. The genetic algorithm (GA) is applied to select a subset of the most discriminate features to remove the irrelevance and redundancy. We use linear discriminant analysis (LDA) as the tool for training the statistical classification model. Experimental results show the proposed approach works well in RNAi screening","PeriodicalId":360097,"journal":{"name":"2006 IEEE/NLM Life Science Systems and Applications Workshop","volume":"12 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2006-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123904086","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 6
An integrated Silicon-on-sapphire Patch-clamp amplifier 集成的蓝宝石硅片箝位放大器
2006 IEEE/NLM Life Science Systems and Applications Workshop Pub Date : 2006-11-30 DOI: 10.1109/LSSA.2006.250429
E. Culurciello, F. Laiwalla, Zhenging Fu, K. Klemic, F. Sigworth
{"title":"An integrated Silicon-on-sapphire Patch-clamp amplifier","authors":"E. Culurciello, F. Laiwalla, Zhenging Fu, K. Klemic, F. Sigworth","doi":"10.1109/LSSA.2006.250429","DOIUrl":"https://doi.org/10.1109/LSSA.2006.250429","url":null,"abstract":"We fabricated an integrated patch-clamp amplifier capable of recording from pico- to tens of micro-amperes of current. The high-dynamic range of seven decades and the pico-ampere sensitivity of the instrument was designed for whole-cell patch-clamp recordings. The prototype was fabricated on a 0.5 mum silicon-on-sapphire process. The device employs an integrating headstage with a frequency-modulated output pulse ranging from 3 Hz to 10 MHz. A digital interface produces a 16bit output conversion of the input currents. We report on electrical measurements from the fabricated device, and measurements conducted on cells in a typical patch-clamp experiment","PeriodicalId":360097,"journal":{"name":"2006 IEEE/NLM Life Science Systems and Applications Workshop","volume":"418 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2006-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126701602","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
Planning for Gene Regulatory Network Intervention 基因调控网络干预计划
2006 IEEE/NLM Life Science Systems and Applications Workshop Pub Date : 2006-11-30 DOI: 10.1109/LSSA.2006.250382
D. Bryce, Seungchan Kim
{"title":"Planning for Gene Regulatory Network Intervention","authors":"D. Bryce, Seungchan Kim","doi":"10.1109/LSSA.2006.250382","DOIUrl":"https://doi.org/10.1109/LSSA.2006.250382","url":null,"abstract":"Modeling the dynamics of cellular processes has recently become a important research area of many disciplines. One of the most important reasons to model a cellular process is to enable high-throughput in-silico experiments that attempt to predict or intervene in the process. These experiments can help accelerate the design of therapies through their cheap replication and alteration. While some techniques exist for reasoning with cellular processes, few take advantage of the flexible and scalable algorithms popularized in AI research. We apply AI planning based search techniques to a well-studied gene regulatory network model and demonstrate its clear advantage over existing methods based on enumeration","PeriodicalId":360097,"journal":{"name":"2006 IEEE/NLM Life Science Systems and Applications Workshop","volume":"613 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2006-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123743166","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 13
An Iterative Approach to Nucleus Segmentation for High Content Imaging in Cancer Research 一种用于肿瘤研究中高含量成像的迭代核分割方法
2006 IEEE/NLM Life Science Systems and Applications Workshop Pub Date : 2006-11-30 DOI: 10.1109/LSSA.2006.250412
A. Tarokh, Kuang-Yu Liu, Xiaobo Zhou, Stephen T. C. Wong
{"title":"An Iterative Approach to Nucleus Segmentation for High Content Imaging in Cancer Research","authors":"A. Tarokh, Kuang-Yu Liu, Xiaobo Zhou, Stephen T. C. Wong","doi":"10.1109/LSSA.2006.250412","DOIUrl":"https://doi.org/10.1109/LSSA.2006.250412","url":null,"abstract":"We present an iterative technique for nucleus segmentation in high throughput RNA interference (RNAi) screening. This technique acts as a crucial processing step towards cell segmentation and feature extraction. Our data comes from three-channel RNAi cell images, with the nucleus information contained in a single DNA channel. Accurate segmentation of the nucleus information provides valuable prior information regarding cell counts and cell positioning, and is thus a valuable prior toward the overall goal of phenotype recognition and detection. Our iterative technique takes direct advantage of image gradient information to obtain accurate nucleus segmentations. It is particularly effective in separating nuclei that are very closely spaced, that thresholding cannot accurately segment","PeriodicalId":360097,"journal":{"name":"2006 IEEE/NLM Life Science Systems and Applications Workshop","volume":"9 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2006-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115595289","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
Segmentation and Tracking of 3D Neuron Microscopy Images using a PDE Based Method and Connected Component Labeling algorithm 基于PDE方法和连通分量标记算法的三维神经元显微图像分割与跟踪
2006 IEEE/NLM Life Science Systems and Applications Workshop Pub Date : 2006-11-30 DOI: 10.1109/LSSA.2006.250432
Yalin Wang, Ilhwan Jo, S. Wong, S. Yau, T. Chan
{"title":"Segmentation and Tracking of 3D Neuron Microscopy Images using a PDE Based Method and Connected Component Labeling algorithm","authors":"Yalin Wang, Ilhwan Jo, S. Wong, S. Yau, T. Chan","doi":"10.1109/LSSA.2006.250432","DOIUrl":"https://doi.org/10.1109/LSSA.2006.250432","url":null,"abstract":"In this paper we introduce our preliminary research results for segmentation and labeling of 3-dimensional microscopy neuron image. We segment each of stacked 2-dimensional image slices using a partial differential equation (PDE) based algorithm and project previous slice segmentation result to the next slide as an initialization condition. Then we label neurons using an efficient connected component labeling algorithm. We show sample results obtained from real neuron image data","PeriodicalId":360097,"journal":{"name":"2006 IEEE/NLM Life Science Systems and Applications Workshop","volume":"12 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2006-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116994044","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 4
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