{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,13]],"date-time":"2026-03-13T02:00:51Z","timestamp":1773367251849,"version":"3.50.1"},"reference-count":20,"publisher":"The Open Journal","issue":"90","license":[{"start":{"date-parts":[[2023,10,2]],"date-time":"2023-10-02T00:00:00Z","timestamp":1696204800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2023,10,2]],"date-time":"2023-10-02T00:00:00Z","timestamp":1696204800000},"content-version":"am","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2023,10,2]],"date-time":"2023-10-02T00:00:00Z","timestamp":1696204800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["JOSS"],"published-print":{"date-parts":[[2023,10,2]]},"DOI":"10.21105\/joss.05563","type":"journal-article","created":{"date-parts":[[2023,10,2]],"date-time":"2023-10-02T07:49:37Z","timestamp":1696232977000},"page":"5563","source":"Crossref","is-referenced-by-count":9,"title":["SMITE: Single Molecule Imaging Toolbox Extraordinaire\n(MATLAB)"],"prefix":"10.21105","volume":"8","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8986-2736","authenticated-orcid":false,"given":"David J.","family":"Schodt","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3520-7605","authenticated-orcid":false,"given":"Michael J.","family":"Wester","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6215-1336","authenticated-orcid":false,"given":"Mohamadreza","family":"Fazel","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6910-5199","authenticated-orcid":false,"given":"Sajjad","family":"Khan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2571-0418","authenticated-orcid":false,"given":"Hanieh","family":"Mazloom-Farsibaf","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-0400-6389","authenticated-orcid":false,"given":"Sandeep","family":"Pallikkuth","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9965-1342","authenticated-orcid":false,"given":"Marjolein B. M.","family":"Meddens","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9939-1923","authenticated-orcid":false,"given":"Farzin","family":"Farzam","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1625-2400","authenticated-orcid":false,"given":"Eric A.","family":"Burns","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5756-9965","authenticated-orcid":false,"given":"William K.","family":"Kanagy","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-8394-3626","authenticated-orcid":false,"given":"Derek A.","family":"Rinaldi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5272-6466","authenticated-orcid":false,"given":"Elton","family":"Jhamba","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1225-0763","authenticated-orcid":false,"given":"Sheng","family":"Liu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6063-6233","authenticated-orcid":false,"given":"Peter K.","family":"Relich","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mark J.","family":"Olah","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stanly L.","family":"Steinberg","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9328-4318","authenticated-orcid":false,"given":"Keith A.","family":"Lidke","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"8722","reference":[{"issue":"18","key":"Lidke_article:2005","doi-asserted-by":"publisher","DOI":"10.1364\/OPEX.13.007052","article-title":"Superresolution by localization of quantum\ndots using blinking statistics","volume":"13","author":"Lidke","year":"2005","unstructured":"Lidke, K. A., Rieger, B., Jovin, T.\nM., & Heintzmann, R. (2005). Superresolution by localization of\nquantum dots using blinking statistics. Optics Express, 13(18),\n7052\u20137062.\nhttps:\/\/doi.org\/10.1364\/OPEX.13.007052","journal-title":"Optics Express"},{"issue":"5793","key":"Betzig_article:2006","doi-asserted-by":"publisher","DOI":"10.1126\/science.1127344","article-title":"Imaging Intracellular Fluorescent Proteins at\nNanometer Resolution","volume":"313","author":"Betzig","year":"2006","unstructured":"Betzig, E., Patterson, G. H.,\nSougrat, R., Lindwasser, O. W., Olenych, S., Bonifacino, J. S.,\nDavidson, M. W., Lippincott-Schwartz, J., & Hess, H. F. (2006).\nImaging Intracellular Fluorescent Proteins at Nanometer Resolution.\nScience, 313(5793), 1642\u20131645.\nhttps:\/\/doi.org\/10.1126\/science.1127344","journal-title":"Science"},{"issue":"10","key":"Rust_article:2006","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth929","article-title":"Sub-diffraction-limit imaging by stochastic\noptical reconstruction microscopy (STORM)","volume":"3","author":"Rust","year":"2006","unstructured":"Rust, M. J., Bates, M., & Zhuang,\nX. (2006). Sub-diffraction-limit imaging by stochastic optical\nreconstruction microscopy (STORM). Nature Methods, 3(10), 793\u2013796.\nhttps:\/\/doi.org\/10.1038\/nmeth929","journal-title":"Nature Methods"},{"issue":"5828","key":"Hell_article:2007","doi-asserted-by":"publisher","DOI":"10.1126\/science.1137395","article-title":"Far-Field Optical Nanoscopy","volume":"316","author":"Hell","year":"2007","unstructured":"Hell, S. W. (2007). Far-Field Optical\nNanoscopy. Science, 316(5828), 1153\u20131158.\nhttps:\/\/doi.org\/10.1126\/science.1137395","journal-title":"Science"},{"issue":"6(7)","key":"vandeLinde_article:2011","doi-asserted-by":"publisher","DOI":"10.1038\/nprot.2011.336","article-title":"Direct stochastic optical reconstruction\nmicroscopy with standard fluorescent probes","volume":"16","author":"van de Linde","year":"2011","unstructured":"van de Linde, S., Loschberger, A.,\nKlein, T., Heidbreder, M., Wolter, S., Heilemann, M., & Sauer, M.\n(2011). Direct stochastic optical reconstruction microscopy with\nstandard fluorescent probes. Nature Protocols, 16(6(7)), 991\u20131009.\nhttps:\/\/doi.org\/10.1038\/nprot.2011.336","journal-title":"Nature Protocols"},{"issue":"1","key":"Fazel_article:2022","doi-asserted-by":"publisher","DOI":"10.1063\/5.0069349","article-title":"Analysis of Super-resolution Single Molecule\nLocalization Microscopy Data: a tutorial","volume":"12","author":"Fazel","year":"2022","unstructured":"Fazel, M., & Wester, M. J.\n(2022). Analysis of Super-resolution Single Molecule Localization\nMicroscopy Data: a tutorial. AIP Advances, 12(1), 010701-1-010701-29.\nhttps:\/\/doi.org\/10.1063\/5.0069349","journal-title":"AIP Advances"},{"issue":"11","key":"Shen_article:2017","doi-asserted-by":"publisher","DOI":"10.1021\/acs.chemrev.6b00815","article-title":"Single Particle Tracking: From Theory to\nBiophysical Applications","volume":"117","author":"Shen","year":"2017","unstructured":"Shen, H., Tauzin, L. J., Baiyasi, R.,\nWang, W., Moringo, N., Shuang, B., & Landes, C. F. (2017). Single\nParticle Tracking: From Theory to Biophysical Applications. Chemical\nReviews, 117(11), 7331--7376.\nhttps:\/\/doi.org\/10.1021\/acs.chemrev.6b00815","journal-title":"Chemical Reviews"},{"issue":"3, Supplement 1","key":"Pallikkuth_article:2018","doi-asserted-by":"publisher","DOI":"10.1016\/j.bpj.2017.11.2912","article-title":"A MATLAB-based Instrument Control Package for\nFluorescence Imaging","volume":"114","author":"Pallikkuth","year":"2018","unstructured":"Pallikkuth, S., Meddens, M., Fazel,\nM., Farsibaf, H., Farzam, F., Wester, M., & Lidke, K. (2018). A\nMATLAB-based Instrument Control Package for Fluorescence Imaging.\nBiophysical Journal, 114(3, Supplement 1), 532a.\nhttps:\/\/doi.org\/10.1016\/j.bpj.2017.11.2912","journal-title":"Biophysical Journal"},{"issue":"5","key":"Smith_article:2010","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.1449","article-title":"Fast, single-molecule localization that\nachieves theoretically minimum uncertainty","volume":"7","author":"Smith","year":"2010","unstructured":"Smith, C. S., Joseph, N., Rieger, B.,\n& Lidke, K. A. (2010). Fast, single-molecule localization that\nachieves theoretically minimum uncertainty. Nature Methods, 7(5).\nhttps:\/\/doi.org\/10.1038\/nmeth.1449","journal-title":"Nature Methods"},{"issue":"7152","key":"Fazel_article:2022a","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-34894-2","article-title":"High-Precision Estimation of Emitter\nPositions using Bayesian Grouping of Localizations","volume":"13","author":"Fazel","year":"2022","unstructured":"Fazel, M., Wester, M. J., Schodt, D.\nJ., Restrepo Cruz, S., Strauss, S., Schueder, F., Schlichthaerle, T.,\nGillette, J. M., Lidke, D. S., Rieger, B., Jungmann, R., & Lidke, K.\nA. (2022). High-Precision Estimation of Emitter Positions using Bayesian\nGrouping of Localizations. Nature Communications, 13(7152), 1\u201311.\nhttps:\/\/doi.org\/10.1038\/s41467-022-34894-2","journal-title":"Nature Communications"},{"issue":"23672","key":"Wester_article:2021","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-021-02850-7","article-title":"Robust, fiducial-free drift correction for\nsuper-resolution imaging","volume":"11","author":"Wester","year":"2021","unstructured":"Wester, M. J., Schodt, D. J.,\nMazloom-Farsibaf, H., Fazel, M., Pallikkuth, S., & Lidke, K. A.\n(2021). Robust, fiducial-free drift correction for super-resolution\nimaging. Scientific Reports, 11(23672), 1\u201314.\nhttps:\/\/doi.org\/10.1038\/s41598-021-02850-7","journal-title":"Scientific Reports"},{"key":"Schodt_article:2021","doi-asserted-by":"publisher","DOI":"10.3389\/fbinf.2021.724325","article-title":"Spatiotemporal Clustering of Repeated\nSuper-Resolution Localizations via Linear Assignment\nProblem","volume":"1","author":"Schodt","year":"2021","unstructured":"Schodt, D. J., & Lidke, K. A.\n(2021). Spatiotemporal Clustering of Repeated Super-Resolution\nLocalizations via Linear Assignment Problem. Frontiers in\nBioinformatics, 1, 57.\nhttps:\/\/doi.org\/10.3389\/fbinf.2021.724325","journal-title":"Frontiers in Bioinformatics","ISSN":"https:\/\/id.crossref.org\/issn\/2673-7647","issn-type":"print"},{"issue":"4","key":"Relich_article:2016","doi-asserted-by":"publisher","DOI":"10.1103\/PhysRevE.93.042401","article-title":"Estimation of the diffusion constant from\nintermittent trajectories with variable position\nuncertainties","volume":"93","author":"Relich","year":"2016","unstructured":"Relich, P. K., Olah, M. J., Cutler,\nP. J., & Lidke, K. A. (2016). Estimation of the diffusion constant\nfrom intermittent trajectories with variable position uncertainties.\nPhysical Review E, 93(4), 042401.\nhttps:\/\/doi.org\/10.1103\/PhysRevE.93.042401","journal-title":"Physical Review E"},{"key":"FrancoNitta_article:2021","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.63678","article-title":"EGFR transactivates RON to drive oncogenic\ncrosstalk","volume":"10","author":"Franco Nitta","year":"2021","unstructured":"Franco Nitta, C., Green, E. W.,\nJhamba, E. D., Keth, J. M., Ortiz-Caraveo, I., Grattan, R. M., Schodt,\nD. J., Gibson, A. C., Rajput, A., Lidke, K. A., Wilson, B. S.,\nSteinkamp, M. P., & Lidke, D. S. (2021). EGFR transactivates RON to\ndrive oncogenic crosstalk. eLife, 10, e63678: 1\u201327.\nhttps:\/\/doi.org\/10.7554\/eLife.63678","journal-title":"eLife"},{"issue":"1","key":"Mazloom-Farsibaf_article:2021","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0246138","article-title":"Comparing lifeact and phalloidin for\nsuper-resolution imaging of actin in fixed cells","volume":"16","author":"Mazloom Farsibaf","year":"2021","unstructured":"Mazloom Farsibaf, H., Farzam, F.,\nFazel, M., Wester, M. J., Meddens, M. B. M., & Lidke, K. A. (2021).\nComparing lifeact and phalloidin for super-resolution imaging of actin\nin fixed cells. PLoS ONE, 16(1), e0246138.\nhttps:\/\/doi.org\/10.1371\/journal.pone.0246138","journal-title":"PLoS ONE"},{"issue":"184","key":"Bailey_article:2022","doi-asserted-by":"publisher","DOI":"10.3791\/63665","article-title":"Quantification of protein phosphorylation\nusing single molecule pull-down (SiMPull)","author":"Bailey","year":"2022","unstructured":"Bailey, E. M., Salazar-Cavazos, E.,\nGrattan, R. M., Wester, M. J., Schodt, D. J., Rojo, J., Lidke, K. A.,\n& Lidke, D. S. (2022). Quantification of protein phosphorylation\nusing single molecule pull-down (SiMPull). Journal of Visualized\nExperiments, 184, e63665: 1\u201320.\nhttps:\/\/doi.org\/10.3791\/63665","journal-title":"Journal of Visualized\nExperiments"},{"issue":"1","key":"Schodt_article:2023","doi-asserted-by":"publisher","DOI":"10.1364\/BOE.477501","article-title":"Automated multi-target super-resolution\nmicroscopy with trust regions","volume":"14","author":"Schodt","year":"2023","unstructured":"Schodt, D. J., Farzam, F., Liu, S.,\n& Lidke, K. A. (2023). Automated multi-target super-resolution\nmicroscopy with trust regions. Biomedical Optics Express, 14(1),\n429\u2013440. https:\/\/doi.org\/10.1364\/BOE.477501","journal-title":"Biomedical Optics Express"},{"key":"Pallikkuth_data:2018","doi-asserted-by":"publisher","DOI":"10.25827\/CS2A-DH13","article-title":"Supporting data for Sequential\nSuper-Resolution Imaging using DNA Strand Displacement [Data\nset]","author":"Pallikkuth","year":"2018","unstructured":"Pallikkuth, S., Martin, C., Farzam,\nF., Edwards, J. S., Lakin, M. R., Lidke, D. S., & Lidke, K. A.\n(2018). Supporting data for Sequential Super-Resolution Imaging using\nDNA Strand Displacement [Data set]. In University of New Mexico Digital\nRepository. University of New Mexico.\nhttps:\/\/doi.org\/10.25827\/CS2A-DH13","journal-title":"University of New Mexico Digital\nRepository"},{"key":"Ries_article:2020","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-020-0938-1","article-title":"SMAP: a modular super-resolution microscopy\nanalysis platform for SMLM data","volume":"17","author":"Ries","year":"2020","unstructured":"Ries, J. (2020). SMAP: a modular\nsuper-resolution microscopy analysis platform for SMLM data. Nature\nMethods, 17, 370\u2013372.\nhttps:\/\/doi.org\/10.1038\/s41592-020-0938-1","journal-title":"Nature Methods"},{"issue":"2","key":"Edelstein_article:2014","doi-asserted-by":"publisher","DOI":"10.14440\/jbm.2014.36","article-title":"Advanced methods of microscope control using\n\\muManager software","volume":"1","author":"Edelstein","year":"2014","unstructured":"Edelstein, A. D., Tsuchida, M. A.,\nAmodaj, N., Pinkard, H., Vale, R. D., & Stuurman, N. (2014).\nAdvanced methods of microscope control using \\muManager software.\nJournal of Biological Methods, 1(2), e11.\nhttps:\/\/doi.org\/10.14440\/jbm.2014.36","journal-title":"Journal of Biological Methods"}],"container-title":["Journal of Open Source Software"],"original-title":[],"link":[{"URL":"https:\/\/joss.theoj.org\/papers\/10.21105\/joss.05563.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2023,10,4]],"date-time":"2023-10-04T06:09:15Z","timestamp":1696399755000},"score":1,"resource":{"primary":{"URL":"https:\/\/joss.theoj.org\/papers\/10.21105\/joss.05563"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,10,2]]},"references-count":20,"journal-issue":{"issue":"90","published-online":{"date-parts":[[2023,10]]}},"alternative-id":["10.21105\/joss.05563"],"URL":"https:\/\/doi.org\/10.21105\/joss.05563","relation":{"has-review":[{"id-type":"uri","id":"https:\/\/github.com\/openjournals\/joss-reviews\/issues\/5563","asserted-by":"subject"}],"references":[{"id-type":"doi","id":"10.5281\/zenodo.8327409","asserted-by":"subject"}]},"ISSN":["2475-9066"],"issn-type":[{"value":"2475-9066","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,10,2]]}}}