{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,20]],"date-time":"2025-09-20T19:09:27Z","timestamp":1758395367895,"version":"3.37.3"},"reference-count":17,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2017,9,4]],"date-time":"2017-09-04T00:00:00Z","timestamp":1504483200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004359","name":"Swedish Research Council","doi-asserted-by":"publisher","award":["VR 2015-04198"],"award-info":[{"award-number":["VR 2015-04198"]}],"id":[{"id":"10.13039\/501100004359","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>SMLocalizer combines the availability of ImageJ with the power of GPU processing for fast and accurate analysis of single molecule localization microscopy data. Analysis of 2D and 3D data in multiple channels is supported.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Plugin freely available for Fiji and ImageJ2.0 through https:\/\/sourceforge.net\/projects\/smlocalizer\/. Plugin also available for continuous updates through ImageJ update system, add http:\/\/sites.imagej.net\/Cellular-Biophysics-KTH\/ as update site in ImageJ. Java and CUDA source code freely available on the web at https:\/\/github.com\/KristofferBernhem\/SMlocalizer.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx553","type":"journal-article","created":{"date-parts":[[2017,9,1]],"date-time":"2017-09-01T11:10:21Z","timestamp":1504264221000},"page":"137-138","source":"Crossref","is-referenced-by-count":11,"title":["SMLocalizer, a GPU accelerated ImageJ plugin for single molecule localization microscopy"],"prefix":"10.1093","volume":"34","author":[{"given":"Kristoffer","family":"Bernhem","sequence":"first","affiliation":[{"name":"Science for Life Laboratory, Department of Applied Physics, Royal Institute of Technology, Stockholm, Sweden"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0578-4003","authenticated-orcid":false,"given":"Hjalmar","family":"Brismar","sequence":"additional","affiliation":[{"name":"Science for Life Laboratory, Department of Applied Physics, Royal Institute of Technology, Stockholm, Sweden"},{"name":"Science for Life Laboratory, Department of Women\u2019s and Children\u2019s Health, Karolinska Institutet, Stockholm, Sweden"}]}],"member":"286","published-online":{"date-parts":[[2017,9,4]]},"reference":[{"key":"2023020208405659200_btx553-B1","doi-asserted-by":"crossref","first-page":"589","DOI":"10.1007\/s12274-011-0115-z","article-title":"Three-dimensional sub-100\u2009nm super-resolution imaging of biological samples using a phase ramp in the objective pupil","volume":"4","author":"Baddeley","year":"2011","journal-title":"Nano Res"},{"key":"2023020208405659200_btx553-B2","doi-asserted-by":"crossref","first-page":"1642","DOI":"10.1126\/science.1127344","article-title":"Imaging intracellular fluorescent proteins at nanometer resolution","volume":"313","author":"Betzig","year":"2006","journal-title":"Science"},{"key":"2023020208405659200_btx553-B3","doi-asserted-by":"crossref","first-page":"943","DOI":"10.1038\/nmeth.1257","article-title":"Fluorescence nanoscopy by ground-state depletion and single-molecule return","volume":"5","author":"Folling","year":"2008","journal-title":"Nat. Methods"},{"key":"2023020208405659200_btx553-B4","doi-asserted-by":"crossref","first-page":"6903","DOI":"10.1002\/anie.200902073","article-title":"Super-resolution imaging with small organic fluorophores","volume":"48","author":"Heilemann","year":"2009","journal-title":"Angew. Chem. Int. Ed"},{"key":"2023020208405659200_btx553-B5","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1038\/nmeth0510-339","article-title":"QuickPALM: 3D real-time photoactivation nanoscopy image processing in ImageJ","volume":"7","author":"Henriques","year":"2010","journal-title":"Nat. Methods"},{"key":"2023020208405659200_btx553-B6","doi-asserted-by":"crossref","first-page":"4258","DOI":"10.1529\/biophysj.106.091116","article-title":"Ultra-high resolution imaging by fluorescence photoactivation localization microscopy","volume":"91","author":"Hess","year":"2006","journal-title":"Biophys. J"},{"key":"2023020208405659200_btx553-B7","doi-asserted-by":"crossref","first-page":"3854","DOI":"10.1038\/srep03854","article-title":"The fidelity of stochastic single-molecule super-resolution reconstructions critically depends upon robust background estimation","volume":"4","author":"Hoogendoorn","year":"2014","journal-title":"Sci. Rep"},{"key":"2023020208405659200_btx553-B8","doi-asserted-by":"crossref","first-page":"810","DOI":"10.1126\/science.1153529","article-title":"Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy","volume":"319","author":"Huang","year":"2008","journal-title":"Science"},{"key":"2023020208405659200_btx553-B9","doi-asserted-by":"crossref","first-page":"527","DOI":"10.1038\/nmeth.1211","article-title":"Three-dimensional sub-100\u2009nm resolution fluorescence microscopy of thick samples","volume":"5","author":"Juette","year":"2008","journal-title":"Nat. Methods"},{"key":"2023020208405659200_btx553-B10","doi-asserted-by":"crossref","first-page":"2389","DOI":"10.1093\/bioinformatics\/btu202","article-title":"ThunderSTORM: a comprehensive ImageJ plug-in for PALM and STORM data analysis and super-resolution imaging","volume":"30","author":"Ovesn\u00fd","year":"2014","journal-title":"Bioinformatics"},{"key":"2023020208405659200_btx553-B11","doi-asserted-by":"crossref","first-page":"2995","DOI":"10.1073\/pnas.0900245106","article-title":"Three-dimensional, single-molecule fluorescence imaging beyond the diffraction limit by using a double-helix point spread function","volume":"106","author":"Pavani","year":"2009","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023020208405659200_btx553-B12","doi-asserted-by":"crossref","first-page":"793","DOI":"10.1038\/nmeth929","article-title":"Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM)","volume":"3","author":"Rust","year":"2006","journal-title":"Nat. Methods"},{"key":"2023020208405659200_btx553-B13","doi-asserted-by":"crossref","first-page":"717","DOI":"10.1038\/nmeth.3442","article-title":"Quantitative evaluation of software packages for single-molecule localization microscopy","volume":"12","author":"Sage","year":"2015","journal-title":"Nat. Methods"},{"key":"2023020208405659200_btx553-B14","doi-asserted-by":"crossref","first-page":"676","DOI":"10.1038\/nmeth.2019","article-title":"Fiji: an open-source platform for biological-image analysis","volume":"9","author":"Schindelin","year":"2012","journal-title":"Nat. Methods"},{"key":"2023020208405659200_btx553-B15","doi-asserted-by":"crossref","first-page":"518","DOI":"10.1002\/mrd.22489","article-title":"The ImageJ ecosystem: An open platform for biomedical image analysis","volume":"82","author":"Schindelin","year":"2015","journal-title":"Mol. Reprod. Dev"},{"key":"2023020208405659200_btx553-B16","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1109\/79.799930","article-title":"A perfect fit for signal and image processing","volume":"16","author":"Unser","year":"1999","journal-title":"IEEE Signal Process. Mag"},{"key":"2023020208405659200_btx553-B17","doi-asserted-by":"crossref","first-page":"7924.","DOI":"10.1038\/srep07924","article-title":"Image artifacts in Single Molecule Localization Microscopy: why optimization of sample preparation protocols matters","volume":"5","author":"Whelan","year":"2015","journal-title":"Sci. Rep"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/1\/137\/49043469\/bioinformatics_34_1_137.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/1\/137\/49043469\/bioinformatics_34_1_137.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T08:52:30Z","timestamp":1675327950000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/34\/1\/137\/4103397"}},"subtitle":[],"editor":[{"given":"Robert","family":"Murphy","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2017,9,4]]},"references-count":17,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2018,1,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btx553","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2018,1,1]]},"published":{"date-parts":[[2017,9,4]]}}}