{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,26]],"date-time":"2026-06-26T22:26:44Z","timestamp":1782512804595,"version":"3.54.5"},"reference-count":25,"publisher":"Oxford University Press (OUP)","issue":"17","license":[{"start":{"date-parts":[[2021,2,27]],"date-time":"2021-02-27T00:00:00Z","timestamp":1614384000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Laboratory Directed Research and Development program at Sandia National Laboratories"},{"name":"National Technology and Engineering Solutions of Sandia, LLC"},{"name":"Honeywell International, Inc., for the U.S. Department of Energy\u2019s National Nuclear Security Administration","award":["DE-NA0003525"],"award-info":[{"award-number":["DE-NA0003525"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,9,9]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Many recent advancements in single-molecule localization microscopy exploit the stochastic photoswitching of fluorophores to reveal complex cellular structures beyond the classical diffraction limit. However, this same stochasticity makes counting the number of molecules to high precision extremely challenging, preventing key insight into the cellular structures and processes under observation.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Modelling the photoswitching behaviour of a fluorophore as an unobserved continuous time Markov process transitioning between a single fluorescent and multiple dark states, and fully mitigating for missed blinks and false positives, we present a method for computing the exact probability distribution for the number of observed localizations from a single photoswitching fluorophore. This is then extended to provide the probability distribution for the number of localizations in a direct stochastic optical reconstruction microscopy experiment involving an arbitrary number of molecules. We demonstrate that when training data are available to estimate photoswitching rates, the unknown number of molecules can be accurately recovered from the posterior mode of the number of molecules given the number of localizations. Finally, we demonstrate the method on experimental data by quantifying the number of adapter protein linker for activation of T cells on the cell surface of the T-cell immunological synapse.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Software and data available at https:\/\/github.com\/lp1611\/mol_count_dstorm.<\/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\/btab136","type":"journal-article","created":{"date-parts":[[2021,2,25]],"date-time":"2021-02-25T15:13:14Z","timestamp":1614265994000},"page":"2730-2737","source":"Crossref","is-referenced-by-count":11,"title":["Blinking statistics and molecular counting in direct stochastic reconstruction microscopy (dSTORM)"],"prefix":"10.1093","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3508-0672","authenticated-orcid":false,"given":"Lekha","family":"Patel","sequence":"first","affiliation":[{"name":"Department of Mathematics, Imperial College London, South Kensington Campus , London, UK"},{"name":"Statistical Sciences, Sandia National Laboratories , Albuquerque, NM 87185, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Williamson","sequence":"additional","affiliation":[{"name":"Department of Physics and Randall Centre for Cell and Molecular Biophysics , King\u2019s College London, London, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dylan M.","family":"Owen","sequence":"additional","affiliation":[{"name":"Institute of Immunology and Immunotherapy and Department of Mathematics, University of Birmingham , Birmingham, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8594-9623","authenticated-orcid":false,"given":"Edward A. 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