{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,22]],"date-time":"2026-07-22T05:28:40Z","timestamp":1784698120315,"version":"3.55.0"},"reference-count":34,"publisher":"Oxford University Press (OUP)","issue":"18","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Identifying cells in an image (cell segmentation) is essential for quantitative single-cell biology via optical microscopy. Although a plethora of segmentation methods exists, accurate segmentation is challenging and usually requires problem-specific tailoring of algorithms. In addition, most current segmentation algorithms rely on a few basic approaches that use the gradient field of the image to detect cell boundaries. However, many microscopy protocols can generate images with characteristic intensity profiles at the cell membrane. This has not yet been algorithmically exploited to establish more general segmentation methods.<\/jats:p>\n               <jats:p>Results: We present an automatic cell segmentation method that decodes the information across the cell membrane and guarantees optimal detection of the cell boundaries on a per-cell basis. Graph cuts account for the information of the cell boundaries through directional cross-correlations, and they automatically incorporate spatial constraints. The method accurately segments images of various cell types grown in dense cultures that are acquired with different microscopy techniques. In quantitative benchmarks and comparisons with established methods on synthetic and real images, we demonstrate significantly improved segmentation performance despite cell-shape irregularity, cell-to-cell variability and image noise. As a proof of concept, we monitor the internalization of green fluorescent protein-tagged plasma membrane transporters in single yeast cells.<\/jats:p>\n               <jats:p>Availability and implementation : Matlab code and examples are available at http:\/\/www.csb.ethz.ch\/tools\/cellSegmPackage.zip .<\/jats:p>\n               <jats:p>Contact : sotiris.dimopoulos@gmail.com or joerg.stelling@bsse.ethz.ch<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu302","type":"journal-article","created":{"date-parts":[[2014,5,22]],"date-time":"2014-05-22T01:26:07Z","timestamp":1400721967000},"page":"2644-2651","source":"Crossref","is-referenced-by-count":128,"title":["Accurate cell segmentation in microscopy images using membrane patterns"],"prefix":"10.1093","volume":"30","author":[{"given":"Sotiris","family":"Dimopoulos","sequence":"first","affiliation":[{"name":"1 Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland, 2 Swiss Institute of Bioinformatics, ETH Zurich, 4058 Basel, Switzerland"},{"name":"1 Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland, 2 Swiss Institute of Bioinformatics, ETH Zurich, 4058 Basel, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christian E.","family":"Mayer","sequence":"additional","affiliation":[{"name":"1 Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland, 2 Swiss Institute of Bioinformatics, ETH Zurich, 4058 Basel, Switzerland"},{"name":"1 Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland, 2 Swiss Institute of Bioinformatics, ETH Zurich, 4058 Basel, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fabian","family":"Rudolf","sequence":"additional","affiliation":[{"name":"1 Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland, 2 Swiss Institute of Bioinformatics, ETH Zurich, 4058 Basel, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joerg","family":"Stelling","sequence":"additional","affiliation":[{"name":"1 Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland, 2 Swiss Institute of Bioinformatics, ETH Zurich, 4058 Basel, Switzerland"},{"name":"1 Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland, 2 Swiss Institute of Bioinformatics, ETH Zurich, 4058 Basel, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2014,5,21]]},"reference":[{"key":"2023012711553392200_btu302-B1","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1109\/TBME.2009.2035102","article-title":"Improved automatic detection and segmentation of cell nuclei in histopathology images","volume":"57","author":"Al-Kofahi","year":"2010","journal-title":"IEEE Trans. Biomed. Eng."},{"key":"2023012711553392200_btu302-B2","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1016\/0031-3203(81)90009-1","article-title":"Generalizing the Hough transform to detect arbitrary shapes","volume":"13","author":"Ballard","year":"1981","journal-title":"Pattern Recognit."},{"key":"2023012711553392200_btu302-B3","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1007\/s11263-006-7934-5","article-title":"Graph cuts and efficient ND image segmentation","volume":"70","author":"Boykov","year":"2006","journal-title":"Int. J. Comput. Vis."},{"key":"2023012711553392200_btu302-B4","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1109\/ICCV.2003.1238310","article-title":"Computing geodesics and minimal surfaces via graph cuts","volume-title":"Proceedings of the Ninth IEEE International Conference on Computer Vision, Nice, France","author":"Boykov","year":"2003"},{"key":"2023012711553392200_btu302-B5","doi-asserted-by":"crossref","first-page":"1124","DOI":"10.1109\/TPAMI.2004.60","article-title":"An experimental comparison of min-cut\/max-flow algorithms for energy minimization in vision","volume":"26","author":"Boykov","year":"2004","journal-title":"IEEE Trans. Pattern Anal. Mach. Intell."},{"key":"2023012711553392200_btu302-B6","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1147\/sj.41.0025","article-title":"Algorithm for computer control of a digital plotter","volume":"4","author":"Bresenham","year":"1965","journal-title":"IBM Syst. J."},{"key":"2023012711553392200_btu302-B7","doi-asserted-by":"crossref","first-page":"R100","DOI":"10.1186\/gb-2006-7-10-r100","article-title":"Cellprofiler: image analysis software for identifying and quantifying cell phenotypes","volume":"7","author":"Carpenter","year":"2006","journal-title":"Genome Biol."},{"key":"2023012711553392200_btu302-B8","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1023\/A:1007979827043","article-title":"Geodesic active contours","volume":"22","author":"Caselles","year":"1997","journal-title":"Int. J. Comput. Vis."},{"key":"2023012711553392200_btu302-B9","doi-asserted-by":"crossref","first-page":"266","DOI":"10.1109\/83.902291","article-title":"Active contours without edges","volume":"10","author":"Chan","year":"2001","journal-title":"IEEE Trans. Image Process."},{"key":"2023012711553392200_btu302-B10","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1111\/j.1365-2818.2008.01974.x","article-title":"Constraint factor graph cut\u2013based active contour method for automated cellular image segmentation in RNAi screening","volume":"230","author":"Chen","year":"2008","journal-title":"J. Microsc."},{"key":"2023012711553392200_btu302-B11","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1038\/nature08779","article-title":"Systems survey of endocytosis by multiparametric image analysis","volume":"464","author":"Collinet","year":"2010","journal-title":"Nature"},{"key":"2023012711553392200_btu302-B12","first-page":"410","article-title":"Segmentation of touching cell nuclei using a two-stage graph cut model","volume-title":"Proceedings of 16th Scandinavian Conference, SCIA, 2009, Oslo, Norway","author":"Dan\u011bk","year":"2009"},{"key":"2023012711553392200_btu302-B13","doi-asserted-by":"crossref","first-page":"697","DOI":"10.1038\/nmeth.2084","article-title":"Biological imaging software tools","volume":"9","author":"Eliceiri","year":"2012","journal-title":"Nat. Methods"},{"key":"2023012711553392200_btu302-B14","first-page":"137","article-title":"Detection of hematopoietic stem cells in microscopy images using a bank of ring filters","volume-title":"Proc. IEEE Int. Symp. Biomed. Imaging, Rotterdam, The Netherlands","author":"Eom","year":"2010"},{"key":"2023012711553392200_btu302-B15","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1038\/nmeth1008","article-title":"Single-cell quantification of molecules and rates using open-source microscope-based cytometry","volume":"4","author":"Gordon","year":"2007","journal-title":"Nat. Methods"},{"key":"2023012711553392200_btu302-B16","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1038\/nchembio.958","article-title":"Fluorescent castasterone reveals bri1 signaling from the plasma membrane","volume":"8","author":"Irani","year":"2012","journal-title":"Nat. Chem. Biol."},{"key":"2023012711553392200_btu302-B17","first-page":"535","article-title":"Voronoi-based segmentation of cells on image manifolds","volume-title":"Proceedings of First International Workshop, CVBIA, 2005, Beijing, China","author":"Jones","year":"2005"},{"key":"2023012711553392200_btu302-B18","doi-asserted-by":"crossref","first-page":"1485","DOI":"10.1109\/ICPR.2010.367","article-title":"Live cell segmentation in fluorescence microscopy via graph cut","volume-title":"2010 International Conference on Pattern Recognition, Istanbul, Turkey","author":"Lesk\u00f3","year":"2010"},{"key":"2023012711553392200_btu302-B19","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1371\/journal.pcbi.1003043","article-title":"Bioimage informatics for systems pharmacology","volume":"9","author":"Li","year":"2013","journal-title":"PLoS Comput. Biol."},{"key":"2023012711553392200_btu302-B20","doi-asserted-by":"crossref","first-page":"714","DOI":"10.1016\/j.cell.2008.09.025","article-title":"Arrestin-related ubiquitin-ligase adaptors regulate endocytosis and protein turnover at the cell surface","volume":"135","author":"Lin","year":"2008","journal-title":"Cell"},{"key":"2023012711553392200_btu302-B21","doi-asserted-by":"crossref","first-page":"995","DOI":"10.1109\/TMI.2013.2243463","article-title":"Segmentation and shape tracking of whole fluorescent cells based on the chan-vese model","volume":"32","author":"Ma\u0161ka","year":"2013","journal-title":"IEEE Trans. Med. Imaging"},{"key":"2023012711553392200_btu302-B22","first-page":"1","article-title":"Using CellX to quantify intracellular events","volume":"14","author":"Mayer","year":"2013","journal-title":"Curr. Protoc. Mol. Biol."},{"key":"2023012711553392200_btu302-B23","doi-asserted-by":"crossref","first-page":"140","DOI":"10.1109\/MSP.2012.2204190","article-title":"Cell segmentation: 50 years down the road [life sciences]","volume":"29","author":"Meijering","year":"2012","journal-title":"IEEE Signal Process. Mag."},{"key":"2023012711553392200_btu302-B24","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1016\/0165-1684(94)90060-4","article-title":"Topographic distance and watershed lines","volume":"38","author":"Meyer","year":"1994","journal-title":"Signal Process."},{"key":"2023012711553392200_btu302-B25","volume-title":"Optimum Signal Processing: An Introduction","author":"Orfanidis","year":"1988","edition":"2nd edn"},{"key":"2023012711553392200_btu302-B26","first-page":"23","article-title":"A threshold selection method from gray-level histograms","volume":"11","author":"Otsu","year":"1975","journal-title":"Automatica"},{"key":"2023012711553392200_btu302-B27","doi-asserted-by":"crossref","first-page":"1827","DOI":"10.1093\/bioinformatics\/btn346","article-title":"Bioimage informatics: a new area of engineering biology","volume":"24","author":"Peng","year":"2008","journal-title":"Bioinformatics"},{"key":"2023012711553392200_btu302-B28","first-page":"3","volume-title":"Level Set Methods and Fast Marching Methods","author":"Sethian","year":"1999"},{"key":"2023012711553392200_btu302-B29","doi-asserted-by":"crossref","first-page":"714","DOI":"10.1038\/nmeth.1984","article-title":"An image analysis toolbox for high-throughput \n              C","volume":"9","author":"W\u00e4hlby","year":"2012","journal-title":"elegans assays. Nat. Methods"},{"key":"2023012711553392200_btu302-B30","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1023\/A:1008036829907","article-title":"A level-set approach to 3D reconstruction from range data","volume":"29","author":"Whitaker","year":"1998","journal-title":"Int. J. Comput. Vis."},{"key":"2023012711553392200_btu302-B31","doi-asserted-by":"crossref","first-page":"210","DOI":"10.1016\/j.cviu.2006.11.004","article-title":"Object segmentation using graph cuts based active contours","volume":"107","author":"Xu","year":"2007","journal-title":"Comput. Vis. Image Underst."},{"key":"2023012711553392200_btu302-B32","doi-asserted-by":"crossref","first-page":"465","DOI":"10.1038\/nature11133","article-title":"Rab5 is necessary for the biogenesis of the endolysosomal system \n              in vivo","volume":"485","author":"Zeigerer","year":"2012","journal-title":"Nature"},{"key":"2023012711553392200_btu302-B33","article-title":"Efficiently solving the piecewise constant mumford-shah model using graph cuts","author":"Zeng","year":"2006"},{"key":"2023012711553392200_btu302-B34","doi-asserted-by":"crossref","first-page":"711","DOI":"10.1038\/nmeth.2046","article-title":"Unsupervised modeling of cell morphology dynamics for time-lapse microscopy","volume":"9","author":"Zhong","year":"2012","journal-title":"Nat. Methods"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/18\/2644\/48929266\/bioinformatics_30_18_2644.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/18\/2644\/48929266\/bioinformatics_30_18_2644.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T12:37:12Z","timestamp":1674823032000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/30\/18\/2644\/2475348"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,5,21]]},"references-count":34,"journal-issue":{"issue":"18","published-print":{"date-parts":[[2014,9,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btu302","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2014,9,15]]},"published":{"date-parts":[[2014,5,21]]}}}