{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T10:14:42Z","timestamp":1790763282825,"version":"4.1.0"},"reference-count":30,"publisher":"Wiley","issue":"11-12","license":[{"start":{"date-parts":[[2015,2,6]],"date-time":"2015-02-06T00:00:00Z","timestamp":1423180800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"funder":[{"name":"European research council (ERC) Starter Grant","award":["337187"],"award-info":[{"award-number":["337187"]}]},{"name":"Marie Curie CIG","award":["334303"],"award-info":[{"award-number":["334303"]}]},{"DOI":"10.13039\/501100000341","name":"Arthritis Research UK","doi-asserted-by":"crossref","award":["19652"],"award-info":[{"award-number":["19652"]}],"id":[{"id":"10.13039\/501100000341","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100000341","name":"Arthritis Research UK","doi-asserted-by":"crossref","award":["20525"],"award-info":[{"award-number":["20525"]}],"id":[{"id":"10.13039\/501100000341","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Journal of Biophotonics"],"published-print":{"date-parts":[[2015,11]]},"abstract":"<jats:p>Single\u2010molecule localisation based super\u2010resolution fluorescence imaging produces maps of the coordinates of fluorescent molecules in a region of interest. Cluster analysis algorithms provide information concerning the clustering characteristics of these molecules, often through the generation of cluster heat maps based on local molecular density. The goal of this study was to generate a new cluster analysis method based on a topographic approach. In particular, a topographic map of the level of clustering across a region is generated based on Getis' variant of Ripley's <jats:italic>K<\/jats:italic>\u2010function. By using the relative heights (topographic prominence, TP) of the peaks in the map, cluster characteristics can be identified more accurately than by using previously demonstrated height thresholds. Analogous to geological TP, the concepts of wet and dry TP and topographic isolation are introduced to generate binary maps. The algorithm is validated using simulated and experimental data and found to significantly outperform previous cluster identification methods.\n<jats:boxed-text content-type=\"graphic\" position=\"anchor\"><jats:caption><jats:p>Illustration of the topographic prominence based cluster analysis algorithm.<\/jats:p><\/jats:caption><jats:graphic xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" mimetype=\"image\/png\" position=\"anchor\" specific-use=\"enlarged-web-image\" xlink:href=\"graphic\/jbio201400127-gra-0001-m.png\"><jats:alt-text>magnified image<\/jats:alt-text><jats:caption><jats:p>Illustration of the topographic prominence based cluster analysis algorithm.<\/jats:p><\/jats:caption><\/jats:graphic><\/jats:boxed-text><\/jats:p>","DOI":"10.1002\/jbio.201400127","type":"journal-article","created":{"date-parts":[[2015,2,6]],"date-time":"2015-02-06T10:08:51Z","timestamp":1423217331000},"page":"925-934","source":"Crossref","is-referenced-by-count":27,"title":["Topographic prominence as a method for cluster identification in single\u2010molecule localisation data"],"prefix":"10.1002","volume":"8","author":[{"given":"Juliette","family":"Griffi\u00e9","sequence":"first","affiliation":[{"name":"Department of Physics and Randall Division of Cell and Molecular Biophysics King's College London  Hodgkin Building, Guy's Campus London SE1 1UL United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lies","family":"Boelen","sequence":"additional","affiliation":[{"name":"Section of Immunology, Division of Infectious Diseases, Faculty of Medicine Imperial College London  Praed Street, St Mary's Campus London United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Garth","family":"Burn","sequence":"additional","affiliation":[{"name":"Department of Physics and Randall Division of Cell and Molecular Biophysics King's College London  Hodgkin Building, Guy's Campus London SE1 1UL United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew P.","family":"Cope","sequence":"additional","affiliation":[{"name":"Academic Department of Rheumatology, Division of Immunology, Infection and Inflammatory Disease, Faculty of Life Sciences and Medicine King's College London  New Hunt's House, Guy's Campus London SE1 1UL United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dylan M.","family":"Owen","sequence":"additional","affiliation":[{"name":"Department of Physics and Randall Division of Cell and Molecular Biophysics King's College London  Hodgkin Building, Guy's Campus London SE1 1UL United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2015,2,6]]},"reference":[{"key":"e_1_2_7_2_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.1127344"},{"key":"e_1_2_7_3_1","doi-asserted-by":"publisher","DOI":"10.1529\/biophysj.106.091116"},{"key":"e_1_2_7_4_1","first-page":"793","volume":"3","author":"Rust M. J.","year":"2006","journal-title":"Meth"},{"key":"e_1_2_7_5_1","doi-asserted-by":"publisher","DOI":"10.1002\/anie.200802376"},{"key":"e_1_2_7_6_1","doi-asserted-by":"publisher","DOI":"10.1002\/jbio.200900089"},{"key":"e_1_2_7_7_1","doi-asserted-by":"publisher","DOI":"10.1038\/ni.2049"},{"key":"e_1_2_7_8_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.bpj.2013.05.063"},{"key":"e_1_2_7_9_1","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.1704"},{"key":"e_1_2_7_10_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0031457"},{"key":"e_1_2_7_11_1","doi-asserted-by":"publisher","DOI":"10.1038\/ni.2488"},{"key":"e_1_2_7_12_1","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms2273"},{"key":"e_1_2_7_13_1","doi-asserted-by":"publisher","DOI":"10.1006\/jasc.2001.0720"},{"key":"e_1_2_7_14_1","doi-asserted-by":"publisher","DOI":"10.2307\/1938452"},{"key":"e_1_2_7_15_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.2517-6161.1977.tb01615.x"},{"key":"e_1_2_7_16_1","doi-asserted-by":"publisher","DOI":"10.1038\/nri2986"},{"key":"e_1_2_7_17_1","doi-asserted-by":"publisher","DOI":"10.1242\/jcs.019117"},{"key":"e_1_2_7_18_1","doi-asserted-by":"publisher","DOI":"10.1056\/NEJM200010053431407"},{"key":"e_1_2_7_19_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ceb.2011.10.004"},{"key":"e_1_2_7_20_1","doi-asserted-by":"publisher","DOI":"10.1034\/j.1600-065X.2003.00075.x"},{"key":"e_1_2_7_21_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.94.8.3909"},{"key":"e_1_2_7_22_1","doi-asserted-by":"publisher","DOI":"10.1038\/sj.emboj.7601959"},{"key":"e_1_2_7_23_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.221463098"},{"key":"e_1_2_7_24_1","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M213234200"},{"key":"e_1_2_7_25_1","doi-asserted-by":"publisher","DOI":"10.1038\/ni950"},{"key":"e_1_2_7_26_1","doi-asserted-by":"publisher","DOI":"10.1083\/jcb.200404160"},{"key":"e_1_2_7_27_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ceb.2003.08.003"},{"key":"e_1_2_7_28_1","doi-asserted-by":"publisher","DOI":"10.1007\/s12154-013-0096-3"},{"key":"e_1_2_7_29_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0945-053X(00)00066-4"},{"key":"e_1_2_7_30_1","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.274.38.26869"},{"key":"e_1_2_7_31_1","doi-asserted-by":"crossref","first-page":"899.835","DOI":"10.1096\/fasebj.21.6.A1226-a","volume":"21","author":"Simon S. I.","year":"2007","journal-title":"FASEB J"}],"container-title":["Journal of Biophotonics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.wiley.com\/onlinelibrary\/tdm\/v1\/articles\/10.1002%2Fjbio.201400127","content-type":"unspecified","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/jbio.201400127","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,10,4]],"date-time":"2023-10-04T06:52:05Z","timestamp":1696402325000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/jbio.201400127"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,2,6]]},"references-count":30,"journal-issue":{"issue":"11-12","published-print":{"date-parts":[[2015,11]]}},"alternative-id":["10.1002\/jbio.201400127"],"URL":"https:\/\/doi.org\/10.1002\/jbio.201400127","archive":["Portico"],"relation":{},"ISSN":["1864-063X","1864-0648"],"issn-type":[{"value":"1864-063X","type":"print"},{"value":"1864-0648","type":"electronic"}],"subject":[],"published":{"date-parts":[[2015,2,6]]}}}