{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:45:54Z","timestamp":1740185154344,"version":"3.37.3"},"reference-count":19,"publisher":"Oxford University Press (OUP)","issue":"21","license":[{"start":{"date-parts":[[2021,5,8]],"date-time":"2021-05-08T00:00:00Z","timestamp":1620432000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"College Research Associateship"},{"DOI":"10.13039\/501100003769","name":"EISAI","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003769","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100017510","name":"UK Dementia Research Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100017510","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Junior Research Fellowship"},{"DOI":"10.13039\/100010663","name":"ERC","doi-asserted-by":"publisher","award":["669237"],"award-info":[{"award-number":["669237"]}],"id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010663","name":"ERC","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,11,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Imaging single molecules has emerged as a powerful characterization tool in the biological sciences. The detection of these under various noise conditions requires the use of algorithms that are dependent on the end-user inputting several parameters, the choice of which can be challenging and subjective.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>In this work, we propose DeepSinse, an easily trainable and useable deep neural network that can detect single molecules with little human input and across a wide range of signal-to-noise ratios. We validate the neural network on the detection of single bursts in simulated and experimental data and compare its performance with the best-in-class, domain-specific algorithms.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availabilityand implementation<\/jats:title>\n                  <jats:p>Ground truth ROI simulating code, neural network training, validation code, classification code, ROI picker, GUI for simulating, training and validating DeepSinse as well as pre-trained networks are all released under the MIT License on www.github.com\/jdanial\/DeepSinse. The dSTORM dataset processing code is released under the MIT License on www.github.com\/jdanial\/StormProcessor.<\/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\/btab352","type":"journal-article","created":{"date-parts":[[2021,5,6]],"date-time":"2021-05-06T13:39:37Z","timestamp":1620308377000},"page":"3998-4000","source":"Crossref","is-referenced-by-count":4,"title":["DeepSinse: deep learning-based detection of single molecules"],"prefix":"10.1093","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9882-8441","authenticated-orcid":false,"given":"John S H","family":"Danial","sequence":"first","affiliation":[{"name":"Yusuf Hamied Department of Chemistry, University of Cambridge , Cambridge CB2 1EW, UK"},{"name":"UK Dementia Research Institute, University of Cambridge , Cambridge CB2 0AH, UK"}]},{"given":"Raed","family":"Shalaby","sequence":"additional","affiliation":[{"name":"Institute of Genetics, University of Cologne , Cologne D-50674, Germany"}]},{"given":"Katia","family":"Cosentino","sequence":"additional","affiliation":[{"name":"Department of Biology, University of Osnabruck , Osnabruck 49076, Germany"}]},{"given":"Marwa M","family":"Mahmoud","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Cambridge , Cambridge CB3 0FD, UK"}]},{"given":"Fady","family":"Medhat","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of York , York YO10 5GH, UK"}]},{"given":"David","family":"Klenerman","sequence":"additional","affiliation":[{"name":"Yusuf Hamied Department of Chemistry, University of Cambridge , Cambridge CB2 1EW, UK"},{"name":"UK Dementia Research Institute, University of Cambridge , Cambridge CB2 0AH, UK"}]},{"given":"Ana J","family":"Garcia Saez","sequence":"additional","affiliation":[{"name":"Institute of Genetics, University of Cologne , Cologne D-50674, Germany"}]}],"member":"286","published-online":{"date-parts":[[2021,5,8]]},"reference":[{"key":"2023051607345566500_btab352-B1","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":"2023051607345566500_btab352-B2","doi-asserted-by":"crossref","first-page":"442","DOI":"10.1126\/science.1088525","article-title":"Diffusion dynamics of glycine receptors revealed by single-quantum dot tracking","volume":"302","author":"Dahan","year":"2003","journal-title":"Science"},{"key":"2023051607345566500_btab352-B3","doi-asserted-by":"crossref","first-page":"994","DOI":"10.1002\/cbic.200600474","article-title":"Membrane protein stoichiometry determined from the step-wise photobleaching of dye-labelled subunits","volume":"8","author":"Das","year":"2007","journal-title":"ChemBioChem"},{"key":"2023051607345566500_btab352-B4","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1006\/meth.2001.1217","article-title":"Single-molecule fluorescence resonance energy transfer","volume":"25","author":"Ha","year":"2001","journal-title":"Methods"},{"key":"2023051607345566500_btab352-B5","doi-asserted-by":"crossref","first-page":"6172","DOI":"10.1002\/anie.200802376","article-title":"Subdiffraction-resolution fluorescence imaging with conventional fluorescent probes","volume":"47","author":"Heilemann","year":"2008","journal-title":"Angew. 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