{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,3,31]],"date-time":"2025-03-31T07:43:42Z","timestamp":1743407022453},"reference-count":25,"publisher":"Oxford University Press (OUP)","issue":"13","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Image analysis, machine learning and statistical modeling have become well established for the automatic recognition and comparison of the subcellular locations of proteins in microscope images. By using a comprehensive set of features describing static images, major subcellular patterns can be distinguished with near perfect accuracy. We now extend this work to time series images, which contain both spatial and temporal information. The goal is to use temporal features to improve recognition of protein patterns that are not fully distinguishable by their static features alone.<\/jats:p>\n               <jats:p>Results: We have adopted and designed five sets of features for capturing temporal behavior in 2D time series images, based on object tracking, temporal texture, normal flow, Fourier transforms and autoregression. Classification accuracy on an image collection for 12 fluorescently tagged proteins was increased when temporal features were used in addition to static features. Temporal texture, normal flow and Fourier transform features were most effective at increasing classification accuracy. We therefore extended these three feature sets to 3D time series images, but observed no significant improvement over results for 2D images. The methods for 2D and 3D temporal pattern analysis do not require segmentation of images into single cell regions, and are suitable for automated high-throughput microscopy applications.<\/jats:p>\n               <jats:p>Availability: Images, source code and results will be available upon publication at http:\/\/murphylab.web.cmu.edu\/software<\/jats:p>\n               <jats:p>Contact: \u00a0murphy@cmu.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq239","type":"journal-article","created":{"date-parts":[[2010,5,20]],"date-time":"2010-05-20T00:58:24Z","timestamp":1274317104000},"page":"1630-1636","source":"Crossref","is-referenced-by-count":13,"title":["Automated analysis of protein subcellular location in time series images"],"prefix":"10.1093","volume":"26","author":[{"given":"Yanhua","family":"Hu","sequence":"first","affiliation":[{"name":"1 Center for Bioimage Informatics, 2 Department of Biological Sciences, 3 Department of Biomedical Engineering, 4 Department of Machine Learning, Carnegie Mellon University, Pittsburgh, PA 15213, 5 Division of Science and Mathematics, University of the Virgin Islands, St Thomas, VI 00803 and 6 Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA"},{"name":"1 Center for Bioimage Informatics, 2 Department of Biological Sciences, 3 Department of Biomedical Engineering, 4 Department of Machine Learning, Carnegie Mellon University, Pittsburgh, PA 15213, 5 Division of Science and Mathematics, University of the Virgin Islands, St Thomas, VI 00803 and 6 Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Elvira","family":"Osuna-Highley","sequence":"additional","affiliation":[{"name":"1 Center for Bioimage Informatics, 2 Department of Biological Sciences, 3 Department of Biomedical Engineering, 4 Department of Machine Learning, Carnegie Mellon University, Pittsburgh, PA 15213, 5 Division of Science and Mathematics, University of the Virgin Islands, St Thomas, VI 00803 and 6 Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA"},{"name":"1 Center for Bioimage Informatics, 2 Department of Biological Sciences, 3 Department of Biomedical Engineering, 4 Department of Machine Learning, Carnegie Mellon University, Pittsburgh, PA 15213, 5 Division of Science and Mathematics, University of the Virgin Islands, St Thomas, VI 00803 and 6 Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Juchang","family":"Hua","sequence":"additional","affiliation":[{"name":"1 Center for Bioimage Informatics, 2 Department of Biological Sciences, 3 Department of Biomedical Engineering, 4 Department of Machine Learning, Carnegie Mellon University, Pittsburgh, PA 15213, 5 Division of Science and Mathematics, University of the Virgin Islands, St Thomas, VI 00803 and 6 Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA"},{"name":"1 Center for Bioimage Informatics, 2 Department of Biological Sciences, 3 Department of Biomedical Engineering, 4 Department of Machine Learning, Carnegie Mellon University, Pittsburgh, PA 15213, 5 Division of Science and Mathematics, University of the Virgin Islands, St Thomas, VI 00803 and 6 Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA"},{"name":"1 Center for Bioimage Informatics, 2 Department of Biological Sciences, 3 Department of Biomedical Engineering, 4 Department of Machine Learning, Carnegie Mellon University, Pittsburgh, PA 15213, 5 Division of Science and Mathematics, University of the Virgin Islands, St Thomas, VI 00803 and 6 Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Theodore Scott","family":"Nowicki","sequence":"additional","affiliation":[{"name":"1 Center for Bioimage Informatics, 2 Department of Biological Sciences, 3 Department of Biomedical Engineering, 4 Department of Machine Learning, Carnegie Mellon University, Pittsburgh, PA 15213, 5 Division of Science and Mathematics, University of the Virgin Islands, St Thomas, VI 00803 and 6 Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA"},{"name":"1 Center for Bioimage Informatics, 2 Department of Biological Sciences, 3 Department of Biomedical Engineering, 4 Department of Machine Learning, Carnegie Mellon University, Pittsburgh, PA 15213, 5 Division of Science and Mathematics, University of the Virgin Islands, St Thomas, VI 00803 and 6 Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Robert","family":"Stolz","sequence":"additional","affiliation":[{"name":"1 Center for Bioimage Informatics, 2 Department of Biological Sciences, 3 Department of Biomedical Engineering, 4 Department of Machine Learning, Carnegie Mellon University, Pittsburgh, PA 15213, 5 Division of Science and Mathematics, University of the Virgin Islands, St Thomas, VI 00803 and 6 Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Camille","family":"McKayle","sequence":"additional","affiliation":[{"name":"1 Center for Bioimage Informatics, 2 Department of Biological Sciences, 3 Department of Biomedical Engineering, 4 Department of Machine Learning, Carnegie Mellon University, Pittsburgh, PA 15213, 5 Division of Science and Mathematics, University of the Virgin Islands, St Thomas, VI 00803 and 6 Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Robert F.","family":"Murphy","sequence":"additional","affiliation":[{"name":"1 Center for Bioimage Informatics, 2 Department of Biological Sciences, 3 Department of Biomedical Engineering, 4 Department of Machine Learning, Carnegie Mellon University, Pittsburgh, PA 15213, 5 Division of Science and Mathematics, University of the Virgin Islands, St Thomas, VI 00803 and 6 Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA"},{"name":"1 Center for Bioimage Informatics, 2 Department of Biological Sciences, 3 Department of Biomedical Engineering, 4 Department of Machine Learning, Carnegie Mellon University, Pittsburgh, PA 15213, 5 Division of Science and Mathematics, University of the Virgin Islands, St Thomas, VI 00803 and 6 Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA"},{"name":"1 Center for Bioimage Informatics, 2 Department of Biological Sciences, 3 Department of Biomedical Engineering, 4 Department of Machine Learning, Carnegie Mellon University, Pittsburgh, PA 15213, 5 Division of Science and Mathematics, University of the Virgin Islands, St Thomas, VI 00803 and 6 Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA"},{"name":"1 Center for Bioimage Informatics, 2 Department of Biological Sciences, 3 Department of Biomedical Engineering, 4 Department of Machine Learning, Carnegie Mellon University, Pittsburgh, PA 15213, 5 Division of Science and Mathematics, University of the Virgin Islands, St Thomas, VI 00803 and 6 Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA"},{"name":"1 Center for Bioimage Informatics, 2 Department of Biological Sciences, 3 Department of Biomedical Engineering, 4 Department of Machine Learning, Carnegie Mellon University, Pittsburgh, PA 15213, 5 Division of Science and Mathematics, University of the Virgin Islands, St Thomas, VI 00803 and 6 Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2010,5,19]]},"reference":[{"key":"2023012507561169200_B1","first-page":"905","article-title":"Motion characterization from temporal cooccurrences of local motion-based measures for video indexing","author":"Bouthemy","year":"1998","journal-title":"International Conference on Pattern Recognition (ICPR'98)"},{"key":"2023012507561169200_B2","author":"Chang","year":"2001","journal-title":"LIBSVM: a library for support vector machines."},{"key":"2023012507561169200_B3","doi-asserted-by":"crossref","first-page":"298","DOI":"10.1117\/12.477899","article-title":"Location proteomics - Building subcellular location trees from high resolution 3D fluorescence microscope images of randomly-tagged proteins","volume":"4962","author":"Chen","year":"2003","journal-title":"Proc. SPIE"},{"key":"2023012507561169200_B4","doi-asserted-by":"crossref","first-page":"361","DOI":"10.1146\/annurev.biophys.35.040405.102114","article-title":"Quantitative fluorescent speckle microscopy of cytoskeleton dynamics","volume":"35","author":"Danuser","year":"2006","journal-title":"Annu. Rev. Biophys. Biomol. Struct."},{"key":"2023012507561169200_B5","doi-asserted-by":"crossref","first-page":"1081","DOI":"10.1007\/s10439-007-9254-5","article-title":"Large-scale automated analysis of location patterns in randomly tagged 3T3 cells","volume":"35","author":"Garcia Osuna","year":"2007","journal-title":"Ann. Biomed. Eng."},{"key":"2023012507561169200_B6","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1016\/j.devcel.2006.12.007","article-title":"Automated subcellular location determination and high throughput microscopy","volume":"12","author":"Glory","year":"2007","journal-title":"Dev. Cell"},{"key":"2023012507561169200_B7","doi-asserted-by":"crossref","first-page":"3320","DOI":"10.1091\/mbc.e04-03-0227","article-title":"Cell cycle-dependent regulation of a human DNA helicase that localizes in DNA damage foci","volume":"15","author":"Gu","year":"2004","journal-title":"Mol. Biol. Cell"},{"key":"2023012507561169200_B8","doi-asserted-by":"crossref","first-page":"786","DOI":"10.1109\/PROC.1979.11328","article-title":"Statistical and structural approaches to texture","volume":"67","author":"Haralick","year":"1979","journal-title":"Proc. IEEE"},{"key":"2023012507561169200_B9","first-page":"1028","article-title":"Application of temporal texture features to automated analysis of protein subcellular locations in time series fluorescence microscope images","author":"Hu","year":"2006","journal-title":"2006 IEEE International Symposium on Biomedical Imaging"},{"key":"2023012507561169200_B10","first-page":"1139","article-title":"Automated classification of subcellular patterns in multicell images without segmentation into single cells","author":"Huang","year":"2004","journal-title":"2004 IEEE International Symposium on Biomedical Imaging"},{"key":"2023012507561169200_B11","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1186\/1471-2105-5-78","article-title":"Boosting accuracy of automated classification of fluorescence microscope images for location proteomics","volume":"5","author":"Huang","year":"2004","journal-title":"BMC Bioinformatics"},{"key":"2023012507561169200_B12","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1117\/12.477903","article-title":"Feature reduction for improved recognition of subcellular location patterns in fluorescence microscope images","volume":"4962","author":"Huang","year":"2003","journal-title":"Proc. SPIE"},{"key":"2023012507561169200_B13","doi-asserted-by":"crossref","first-page":"896","DOI":"10.2144\/96205rr03","article-title":"CD-Tagging: a new approach to gene and protein discovery and analysis","volume":"20","author":"Jarvik","year":"1996","journal-title":"BioTechniques"},{"key":"2023012507561169200_B14","doi-asserted-by":"crossref","first-page":"852","DOI":"10.2144\/02334rr02","article-title":"In vivo functional proteomics: mammalian genome annotation using CD-tagging","volume":"33","author":"Jarvik","year":"2002","journal-title":"BioTechniques"},{"key":"2023012507561169200_B15","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1002\/nav.3800020109","article-title":"The hungarian method for the assignment problem","volume":"2","author":"Kuhn","year":"1955","journal-title":"Naval Res. Logistic Quart."},{"key":"2023012507561169200_B16","first-page":"1156","article-title":"Nonuniform temporal alignment of slice sequences for four-dimensional imaging of cyclically deforming embryonic structures","volume-title":"IEEE International Symposium on Biomedical Imaging.","author":"Liebling","year":"2006"},{"key":"2023012507561169200_B17","doi-asserted-by":"crossref","first-page":"2230","DOI":"10.1016\/S0006-3495(99)77379-0","article-title":"Towards objective selection of representative microscope images","volume":"76","author":"Markey","year":"1999","journal-title":"Biophys. J."},{"key":"2023012507561169200_B18","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1023\/B:VLSI.0000003028.71666.44","article-title":"Robust numerical features for description and classification of subcellular location patterns in fluorescence microscope images","volume":"35","author":"Murphy","year":"2003","journal-title":"J. VLSI Sig. Proc."},{"key":"2023012507561169200_B19","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1016\/1049-9660(92)90087-J","article-title":"Qualitative recognition of motion using temporal texture","volume":"56","author":"Nelson","year":"1992","journal-title":"CVGIP Image Understanding"},{"key":"2023012507561169200_B20","first-page":"64","article-title":"Motion retrieval by temporal slices analysis","volume":"4","author":"Ngo","year":"2002","journal-title":"Proc. Int. Conf. Pattern Recognition"},{"key":"2023012507561169200_B21","first-page":"630","article-title":"Picture thresholding using an iterative selection method","author":"Ridler","year":"1978","journal-title":"IEEE Trans. Syst. Man Cybernet., SMC-8"},{"key":"2023012507561169200_B22","doi-asserted-by":"crossref","first-page":"525","DOI":"10.1038\/nmeth892","article-title":"Dynamic proteomics in individual human cells uncovers widespread cell-cycle dependence of nuclear proteins","volume":"3","author":"Sigal","year":"2006","journal-title":"Nat. Methods"},{"key":"2023012507561169200_B23","first-page":"1","article-title":"Cell motin analysis without explicit tracking","volume-title":"Computer Vision and Pattern Recognition.","author":"Souvenir","year":"2008"},{"key":"2023012507561169200_B24","doi-asserted-by":"crossref","first-page":"823","DOI":"10.1109\/ICIP.1996.560871","article-title":"Temporal Texture Modeling","volume":"3","author":"Szummer","year":"1996","journal-title":"IEEE Intl. Conf. On Image Processing"},{"key":"2023012507561169200_B25","doi-asserted-by":"crossref","first-page":"152","DOI":"10.1109\/TITB.2008.2007098","article-title":"A novel cell segmentation method and cell phase identification using Markov model","volume":"13","author":"Zhou","year":"2009","journal-title":"IEEE Trans. Inf. Technol. Biomed."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/13\/1630\/48852475\/bioinformatics_26_13_1630.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/13\/1630\/48852475\/bioinformatics_26_13_1630.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T07:56:39Z","timestamp":1674633399000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/26\/13\/1630\/200221"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,5,19]]},"references-count":25,"journal-issue":{"issue":"13","published-print":{"date-parts":[[2010,7,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btq239","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2010,7,1]]},"published":{"date-parts":[[2010,5,19]]}}}