{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,8]],"date-time":"2026-07-08T04:53:35Z","timestamp":1783486415837,"version":"3.55.0"},"reference-count":45,"publisher":"Springer Science and Business Media LLC","issue":"S16","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2013,10]]},"DOI":"10.1186\/1471-2105-14-s16-s4","type":"journal-article","created":{"date-parts":[[2013,10,22]],"date-time":"2013-10-22T09:06:33Z","timestamp":1382432793000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":29,"title":["cellXpress: a fast and user-friendly software platform for profiling cellular phenotypes"],"prefix":"10.1186","volume":"14","author":[{"given":"Danai","family":"Laksameethanasan","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rui Zhen","family":"Tan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Geraldine Wei-Ling","family":"Toh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lit-Hsin","family":"Loo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2013,10,22]]},"reference":[{"issue":"12","key":"6124_CR1","doi-asserted-by":"publisher","first-page":"1213","DOI":"10.1093\/bioinformatics\/17.12.1213","volume":"17","author":"MV Boland","year":"2001","unstructured":"Boland MV, Murphy RF: A neural network classifier capable of recognizing the patterns of all major subcellular structures in fluorescence microscope images of HeLa cells. Bioinformatics. 2001, 17 (12): 1213-1223. 10.1093\/bioinformatics\/17.12.1213.","journal-title":"Bioinformatics"},{"issue":"5","key":"6124_CR2","doi-asserted-by":"crossref","first-page":"445","DOI":"10.1038\/nmeth1032","volume":"4","author":"LH Loo","year":"2007","unstructured":"Loo LH, Wu LF, Altschuler SJ: Image-based multivariate profiling of drug responses from single cells. Nat Methods. 2007, 4 (5): 445-453.","journal-title":"Nat Methods"},{"issue":"7289","key":"6124_CR3","doi-asserted-by":"publisher","first-page":"721","DOI":"10.1038\/nature08869","volume":"464","author":"B Neumann","year":"2010","unstructured":"Neumann B, Walter T, Heriche JK, Bulkescher J, Erfle H, Conrad C, Rogers P, Poser I, Held M, Liebel U: Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes. Nature. 2010, 464 (7289): 721-727. 10.1038\/nature08869.","journal-title":"Nature"},{"issue":"5832","key":"6124_CR4","doi-asserted-by":"publisher","first-page":"1753","DOI":"10.1126\/science.1140324","volume":"316","author":"C Bakal","year":"2007","unstructured":"Bakal C, Aach J, Church G, Perrimon N: Quantitative morphological signatures define local signaling networks regulating cell morphology. Science. 2007, 316 (5832): 1753-1756. 10.1126\/science.1140324.","journal-title":"Science"},{"issue":"7286","key":"6124_CR5","doi-asserted-by":"publisher","first-page":"243","DOI":"10.1038\/nature08779","volume":"464","author":"C Collinet","year":"2010","unstructured":"Collinet C, Stoter M, Bradshaw CR, Samusik N, Rink JC, Kenski D, Habermann B, Buchholz F, Henschel R, Mueller MS: Systems survey of endocytosis by multiparametric image analysis. Nature. 2010, 464 (7286): 243-249. 10.1038\/nature08779.","journal-title":"Nature"},{"issue":"8","key":"6124_CR6","doi-asserted-by":"publisher","first-page":"1179","DOI":"10.1093\/bioinformatics\/btr095","volume":"27","author":"L Kamentsky","year":"2011","unstructured":"Kamentsky L, Jones TR, Fraser A, Bray MA, Logan DJ, Madden KL, Ljosa V, Rueden C, Eliceiri KW, Carpenter AE: Improved structure, function and compatibility for CellProfiler: modular high-throughput image analysis software. Bioinformatics. 2011, 27 (8): 1179-1180. 10.1093\/bioinformatics\/btr095.","journal-title":"Bioinformatics"},{"issue":"1 Suppl","key":"6124_CR7","doi-asserted-by":"publisher","first-page":"25","DOI":"10.2144\/000112517","volume":"43","author":"TJ Collins","year":"2007","unstructured":"Collins TJ: ImageJ for microscopy. Biotechniques. 2007, 43 (1 Suppl): 25-30.","journal-title":"Biotechniques"},{"issue":"7","key":"6124_CR8","doi-asserted-by":"publisher","first-page":"683","DOI":"10.1038\/nmeth.2047","volume":"9","author":"P Kankaanpaa","year":"2012","unstructured":"Kankaanpaa P, Paavolainen L, Tiitta S, Karjalainen M, Paivarinne J, Nieminen J, Marjomaki V, Heino J, White DJ: BioImageXD: an open, general-purpose and high-throughput image-processing platform. Nature methods. 2012, 9 (7): 683-689. 10.1038\/nmeth.2047.","journal-title":"Nature methods"},{"issue":"7","key":"6124_CR9","doi-asserted-by":"publisher","first-page":"690","DOI":"10.1038\/nmeth.2075","volume":"9","author":"F de Chaumont","year":"2012","unstructured":"de Chaumont F, Dallongeville S, Chenouard N, Herve N, Pop S, Provoost T, Meas-Yedid V, Pankajakshan P, Lecomte T, Le Montagner Y: Icy: an open bioimage informatics platform for extended reproducible research. Nature methods. 2012, 9 (7): 690-696. 10.1038\/nmeth.2075.","journal-title":"Nature methods"},{"issue":"3","key":"6124_CR10","doi-asserted-by":"publisher","first-page":"245","DOI":"10.1038\/nmeth.1896","volume":"9","author":"C Allan","year":"2012","unstructured":"Allan C, Burel JM, Moore J, Blackburn C, Linkert M, Loynton S, Macdonald D, Moore WJ, Neves C, Patterson A: OMERO: flexible, model-driven data management for experimental biology. Nature methods. 2012, 9 (3): 245-253. 10.1038\/nmeth.1896.","journal-title":"Nature methods"},{"issue":"7","key":"6124_CR11","doi-asserted-by":"publisher","first-page":"979","DOI":"10.1093\/bioinformatics\/btq046","volume":"26","author":"G Pau","year":"2010","unstructured":"Pau G, Fuchs F, Sklyar O, Boutros M, Huber W: EBImage--an R package for image processing with applications to cellular phenotypes. Bioinformatics. 2010, 26 (7): 979-981. 10.1093\/bioinformatics\/btq046.","journal-title":"Bioinformatics"},{"key":"6124_CR12","doi-asserted-by":"publisher","first-page":"82","DOI":"10.1186\/1471-2105-9-82","volume":"9","author":"M Fourment","year":"2008","unstructured":"Fourment M, Gillings MR: A comparison of common programming languages used in bioinformatics. BMC Bioinformatics. 2008, 9: 82-10.1186\/1471-2105-9-82.","journal-title":"BMC Bioinformatics"},{"key":"6124_CR13","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1109\/2.876288","volume":"33","author":"L Prechelt","year":"2000","unstructured":"Prechelt L: An empirical comparison of C, C++, Java, Perl, Python, Rexx and Tcl. IEEE Computer. 2000, 33: 23-29. 10.1109\/2.876288.","journal-title":"IEEE Computer"},{"issue":"7","key":"6124_CR14","doi-asserted-by":"publisher","first-page":"567","DOI":"10.1038\/nrd2876","volume":"8","author":"Y Feng","year":"2009","unstructured":"Feng Y, Mitchison TJ, Bender A, Young DW, Tallarico JA: Multi-parameter phenotypic profiling: using cellular effects to characterize small-molecule compounds. Nat Rev Drug Discov. 2009, 8 (7): 567-578. 10.1038\/nrd2876.","journal-title":"Nat Rev Drug Discov"},{"key":"6124_CR15","unstructured":"[http:\/\/www.hdfgroup.org\/HDF5\/]"},{"issue":"11","key":"6124_CR16","first-page":"122","volume":"25","author":"G Bradski","year":"2000","unstructured":"Bradski G: The OpenCV Library. Dr Dobb's Journal of Software Tools. 2000, 25 (11): 122-125.","journal-title":"Dr Dobb's Journal of Software Tools"},{"issue":"4","key":"6124_CR17","doi-asserted-by":"publisher","first-page":"47","DOI":"10.1109\/40.865866","volume":"20","author":"SK Raman","year":"2000","unstructured":"Raman SK, Pentkovski V, Keshava J: Implementing streaming SIMD extensions on the Pentium III processor. IEEE Micro. 2000, 20 (4): 47-57. 10.1109\/40.865866.","journal-title":"IEEE Micro"},{"key":"6124_CR18","unstructured":"[http:\/\/www.openmp.org]"},{"key":"6124_CR19","unstructured":"[http:\/\/www.r-project.org]"},{"key":"6124_CR20","unstructured":"[http:\/\/www.wxwidgets.org]"},{"issue":"3","key":"6124_CR21","doi-asserted-by":"publisher","first-page":"375","DOI":"10.1083\/jcb.200904140","volume":"187","author":"LH Loo","year":"2009","unstructured":"Loo LH, Lin HJ, Singh DK, Lyons KM, Altschuler SJ, Wu LF: Heterogeneity in the physiological states and pharmacological responses of differentiating 3T3-L1 preadipocytes. J Cell Biol. 2009, 187 (3): 375-384. 10.1083\/jcb.200904140.","journal-title":"J Cell Biol"},{"issue":"10","key":"6124_CR22","doi-asserted-by":"publisher","first-page":"759","DOI":"10.1038\/nmeth.1375","volume":"6","author":"LH Loo","year":"2009","unstructured":"Loo LH, Lin HJ, Steininger RJ, Wang Y, Wu LF, Altschuler SJ: An approach for extensibly profiling the molecular states of cellular subpopulations. Nat Methods. 2009, 6 (10): 759-765. 10.1038\/nmeth.1375.","journal-title":"Nat Methods"},{"key":"6124_CR23","doi-asserted-by":"publisher","first-page":"176","DOI":"10.1109\/83.217222","volume":"2","author":"L Vincent","year":"1993","unstructured":"Vincent L: Morphological grayscale reconstruction in image analysis: applications and efficient algorithms. IEEE Trans on Image Processing. 1993, 2: 176-201. 10.1109\/83.217222.","journal-title":"IEEE Trans on Image Processing"},{"key":"6124_CR24","doi-asserted-by":"publisher","first-page":"62","DOI":"10.1109\/TSMC.1979.4310076","volume":"9","author":"N Otsu","year":"1979","unstructured":"Otsu N: A threshold selection method from grey-level histograms. IEEE Trans Systems, Man and Cybernetics. 1979, 9: 62-66.","journal-title":"IEEE Trans Systems, Man and Cybernetics"},{"key":"6124_CR25","doi-asserted-by":"publisher","first-page":"583","DOI":"10.1109\/34.87344","volume":"13","author":"L Vincent","year":"1991","unstructured":"Vincent L, Soille P: Watersheds in digital spaces: an efficient algorithm based on immersion simulations. IEEE Trans on Pattern Analysis and Machine Intelligence. 1991, 13: 583-598. 10.1109\/34.87344.","journal-title":"IEEE Trans on Pattern Analysis and Machine Intelligence"},{"key":"6124_CR26","first-page":"1871","volume":"9","author":"R-E Fan","year":"2008","unstructured":"Fan R-E, Chang K-W, Hsieh C-J, Wang X-R, Lin C-J: LIBLINEAR: A library for large linear classification. Journal of Machine Learning Research. 2008, 9: 1871-1874.","journal-title":"Journal of Machine Learning Research"},{"key":"6124_CR27","unstructured":"[http:\/\/www.cellXpress.org]"},{"key":"6124_CR28","unstructured":"[http:\/\/www.cellprofiler.org]"},{"key":"6124_CR29","unstructured":"[http:\/\/rsbweb.nih.gov\/ij]"},{"key":"6124_CR30","unstructured":"[http:\/\/fiji.sc]"},{"key":"6124_CR31","unstructured":"(downloaded on 1st December 2012), [http:\/\/www.cellprofiler.org\/linked_files\/Examplezips\/ExampleFlyImages.zip]"},{"key":"6124_CR32","unstructured":"(downloaded on 1st December 2012), [http:\/\/www.broadinstitute.org\/bbbc\/BBBC018]"},{"issue":"6","key":"6124_CR33","doi-asserted-by":"publisher","first-page":"1283","DOI":"10.1016\/j.cell.2006.01.040","volume":"124","author":"J Moffat","year":"2006","unstructured":"Moffat J, Grueneberg DA, Yang X, Kim SY, Kloepfer AM, Hinkle G, Piqani B, Eisenhaure TM, Luo B, Grenier JK: A lentiviral RNAi library for human and mouse genes applied to an arrayed viral high-content screen. Cell. 2006, 124 (6): 1283-1298. 10.1016\/j.cell.2006.01.040.","journal-title":"Cell"},{"key":"6124_CR34","unstructured":"(downloaded on 20 Dec 2010), [http:\/\/www.ebi.ac.uk\/huber-srv\/cellmorph]"},{"key":"6124_CR35","doi-asserted-by":"publisher","first-page":"370","DOI":"10.1038\/msb.2010.25","volume":"6","author":"F Fuchs","year":"2010","unstructured":"Fuchs F, Pau G, Kranz D, Sklyar O, Budjan C, Steinbrink S, Horn T, Pedal A, Huber W, Boutros M: Clustering phenotype populations by genome-wide RNAi and multiparametric imaging. Mol Syst Biol. 2010, 6: 370-","journal-title":"Mol Syst Biol"},{"issue":"6","key":"6124_CR36","doi-asserted-by":"publisher","first-page":"a003012","DOI":"10.1101\/cshperspect.a003012","volume":"1","author":"V Bennett","year":"2009","unstructured":"Bennett V, Healy J: Membrane domains based on ankyrin and spectrin associated with cell-cell interactions. Cold Spring Harb Perspect Biol. 2009, 1 (6): a003012-10.1101\/cshperspect.a003012.","journal-title":"Cold Spring Harb Perspect Biol"},{"issue":"6","key":"6124_CR37","doi-asserted-by":"publisher","first-page":"929","DOI":"10.1109\/TPAMI.2007.1046","volume":"29","author":"R Unnikrishnan","year":"2007","unstructured":"Unnikrishnan R, Pantofaru C, Hebert M: Toward objective evaluation of image segmentation algorithms. IEEE Trans Pattern Anal Mach Intell. 2007, 29 (6): 929-944.","journal-title":"IEEE Trans Pattern Anal Mach Intell"},{"issue":"11","key":"6124_CR38","doi-asserted-by":"publisher","first-page":"559","DOI":"10.1080\/14786440109462720","volume":"2","author":"K Pearson","year":"1901","unstructured":"Pearson K: On Lines and Planes of Closest Fit to Systems of Points in Space. Philosophical Magazine. 1901, 2 (11): 559-572. 10.1080\/14786440109462720.","journal-title":"Philosophical Magazine"},{"issue":"5","key":"6124_CR39","doi-asserted-by":"crossref","first-page":"445","DOI":"10.1038\/nmeth1032","volume":"4","author":"LH Loo","year":"2007","unstructured":"Loo LH, Wu LF, Altschuler SJ: Image-based multivariate profiling of drug responses from single cells. Nat Methods. 2007, 4 (5): 445-453.","journal-title":"Nat Methods"},{"key":"6124_CR40","doi-asserted-by":"publisher","DOI":"10.1007\/978-0-387-21706-2","volume-title":"Modern Applied Statistics with S","author":"WN Venables","year":"2002","unstructured":"Venables WN, Ripley BD: Modern Applied Statistics with S. 2002, Springer, New York, 4","edition":"4"},{"key":"6124_CR41","unstructured":"[http:\/\/cran.r-project.org\/web\/packages\/rgl]"},{"issue":"7","key":"6124_CR42","doi-asserted-by":"publisher","first-page":"676","DOI":"10.1038\/nmeth.2019","volume":"9","author":"J Schindelin","year":"2012","unstructured":"Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M, Pietzsch T, Preibisch S, Rueden C, Saalfeld S, Schmid B: Fiji: an open-source platform for biological-image analysis. Nat Methods. 2012, 9 (7): 676-682. 10.1038\/nmeth.2019.","journal-title":"Nat Methods"},{"issue":"10","key":"6124_CR43","doi-asserted-by":"publisher","first-page":"R100","DOI":"10.1186\/gb-2006-7-10-r100","volume":"7","author":"AE Carpenter","year":"2006","unstructured":"Carpenter AE, Jones TR, Lamprecht MR, Clarke C, Kang IH, Friman O, Guertin DA, Chang JH, Lindquist RA, Moffat J: CellProfiler: image analysis software for identifying and quantifying cell phenotypes. Genome Biol. 2006, 7 (10): R100-10.1186\/gb-2006-7-10-r100.","journal-title":"Genome Biol"},{"issue":"4","key":"6124_CR44","doi-asserted-by":"publisher","first-page":"617","DOI":"10.1016\/0031-3203(93)90115-D","volume":"26","author":"C Li","year":"1998","unstructured":"Li C, Lee C: An Iterative Algorithm for Minimum Cross Entropy Thresholding. Pattern Recognition. 1998, 26 (4): 617-625.","journal-title":"Pattern Recognition"},{"issue":"7","key":"6124_CR45","doi-asserted-by":"publisher","first-page":"741","DOI":"10.1177\/25.7.70454","volume":"25","author":"G Zack","year":"1977","unstructured":"Zack G, Rogers W, Latt S: Automatic measurement of sister chromatid exchange frequency. J Histochem Cytochem. 1977, 25 (7): 741-753. 10.1177\/25.7.70454.","journal-title":"J Histochem Cytochem"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-14-S16-S4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,2]],"date-time":"2021-09-02T02:02:47Z","timestamp":1630548167000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-14-S16-S4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,10]]},"references-count":45,"journal-issue":{"issue":"S16","published-print":{"date-parts":[[2013,10]]}},"alternative-id":["6124"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-14-s16-s4","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013,10]]},"assertion":[{"value":"22 October 2013","order":1,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"S4"}}