{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,23]],"date-time":"2025-12-23T18:49:37Z","timestamp":1766515777653,"version":"3.37.3"},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2022,4,28]],"date-time":"2022-04-28T00:00:00Z","timestamp":1651104000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100001665","name":"Agence Nationale de la Recherche","doi-asserted-by":"publisher","award":["ANR-17-CE23-0016","PIA\/ANR-16-CONV-0005","ANR-19-P3IA-0001"],"award-info":[{"award-number":["ANR-17-CE23-0016","PIA\/ANR-16-CONV-0005","ANR-19-P3IA-0001"]}],"id":[{"id":"10.13039\/501100001665","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,5,26]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>Single-molecule localization microscopy allows studying the dynamics of biomolecules in cells and resolving the biophysical properties of the molecules and their environment underlying cellular function. With the continuously growing amount of data produced by individual experiments, the computational cost of quantifying these properties is increasingly becoming the bottleneck of single-molecule analysis. Mining these data requires an integrated and efficient analysis toolbox.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We introduce TRamWAy, a modular Python library that features: (i) a conservative tracking procedure for localization data, (ii) a range of sampling techniques for meshing the spatio-temporal support of the data, (iii) computationally efficient solvers for inverse models, with the option of plugging in user-defined functions and (iv) a collection of analysis tools and a simple web-based interface.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>TRamWAy is a Python library and can be installed with pip and conda. The source code is available at https:\/\/github.com\/DecBayComp\/TRamWAy.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac291","type":"journal-article","created":{"date-parts":[[2022,4,25]],"date-time":"2022-04-25T19:11:59Z","timestamp":1650913919000},"page":"3149-3150","source":"Crossref","is-referenced-by-count":8,"title":["TRamWAy: mapping physical properties of individual biomolecule random motion in large-scale single-particle tracking experiments"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1615-6400","authenticated-orcid":false,"given":"Fran\u00e7ois","family":"Laurent","sequence":"first","affiliation":[{"name":"Decision and Bayesian Computation, Computational Biology Department, Neuroscience Department , CNRS USR 3756, CNRS UMR 3571, Institut Pasteur , Paris 75015, France"},{"name":"Institut Pasteur, Universit\u00e9 Paris Cit\u00e9, Bioinformatics and Biostatistics Hub , Paris F-75015, France"}]},{"given":"Hippolyte","family":"Verdier","sequence":"additional","affiliation":[{"name":"Decision and Bayesian Computation, Computational Biology Department, Neuroscience Department , CNRS USR 3756, CNRS UMR 3571, Institut Pasteur , Paris 75015, France"},{"name":"Histopathology and Bio-Imaging Group, Sanofi R&D , Vitry-Sur-Seine 94400, France"},{"name":"Universit\u00e9 Paris Cit\u00e9, UFR de Physique , Paris 75013, France"}]},{"given":"Maxime","family":"Duval","sequence":"additional","affiliation":[{"name":"Decision and Bayesian Computation, Computational Biology Department, Neuroscience Department , CNRS USR 3756, CNRS UMR 3571, Institut Pasteur , Paris 75015, France"}]},{"given":"Alexander","family":"Serov","sequence":"additional","affiliation":[{"name":"Decision and Bayesian Computation, Computational Biology Department, Neuroscience Department , CNRS USR 3756, CNRS UMR 3571, Institut Pasteur , Paris 75015, France"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5329-475X","authenticated-orcid":false,"given":"Christian L","family":"Vestergaard","sequence":"additional","affiliation":[{"name":"Decision and Bayesian Computation, Computational Biology Department, Neuroscience Department , CNRS USR 3756, CNRS UMR 3571, Institut Pasteur , Paris 75015, France"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5484-9056","authenticated-orcid":false,"given":"Jean-Baptiste","family":"Masson","sequence":"additional","affiliation":[{"name":"Decision and Bayesian Computation, Computational Biology Department, Neuroscience Department , CNRS USR 3756, CNRS UMR 3571, Institut Pasteur , Paris 75015, France"}]}],"member":"286","published-online":{"date-parts":[[2022,4,28]]},"reference":[{"key":"2023041403075540300_","doi-asserted-by":"crossref","first-page":"1209","DOI":"10.1016\/j.bpj.2016.01.018","article-title":"A primer on the Bayesian approach to high-density single-molecule trajectories analysis","volume":"110","author":"Beheiry","year":"2016","journal-title":"Biophys. J"},{"key":"2023041403075540300_","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":"2023041403075540300_","doi-asserted-by":"crossref","first-page":"1100","DOI":"10.1038\/s41592-020-0946-1","article-title":"Genuage: visualize and analyze multidimensional single-molecule point cloud data in virtual reality","volume":"17","author":"Blanc","year":"2020","journal-title":"Nat. Methods"},{"key":"2023041403075540300_","doi-asserted-by":"crossref","first-page":"1136","DOI":"10.1093\/bib\/bbz052","article-title":"An overview of diffusion models for intracellular dynamics analysis","volume":"21","author":"Briane","year":"2020","journal-title":"Brief. Bioinform"},{"key":"2023041403075540300_","doi-asserted-by":"crossref","first-page":"124106","DOI":"10.1063\/1.5144523","article-title":"Inferring effective forces for Langevin dynamics using Gaussian processes","volume":"152","author":"Bryan","year":"2020","journal-title":"J. Chem. Phys"},{"key":"2023041403075540300_","doi-asserted-by":"crossref","first-page":"313a","DOI":"10.1016\/j.bpj.2019.11.1763","article-title":"Bayesian grouping of localizations, sub-nanometer precision, counting and resolution doubling","volume":"118","author":"Fazel","year":"2020","journal-title":"Biophys. J"},{"key":"2023041403075540300_","doi-asserted-by":"crossref","first-page":"16283","DOI":"10.1038\/s41598-018-34536-y","article-title":"Single molecule localisation microscopy reveals how HIV-1 gag proteins sense membrane virus assembly sites in living host CD4 T cells","volume":"8","author":"Floderer","year":"2018","journal-title":"Sci. Rep"},{"volume-title":"Nanoimaging","year":"2012","author":"Giannone","key":"2023041403075540300_"},{"key":"2023041403075540300_","doi-asserted-by":"crossref","first-page":"17052","DOI":"10.1073\/pnas.1204589109","article-title":"Heterogeneity of AMPA receptor trafficking and molecular interactions revealed by superresolution analysis of live cell imaging","volume":"109","author":"Hoze","year":"2012","journal-title":"Proc. Natl. Acad. Sci. U S A"},{"key":"2023041403075540300_","doi-asserted-by":"crossref","first-page":"695","DOI":"10.1038\/nmeth.1237","article-title":"Robust single-particle tracking in live-cell time-lapse sequences","volume":"5","author":"Jaqaman","year":"2008","journal-title":"Nat. Methods"},{"key":"2023041403075540300_","doi-asserted-by":"crossref","first-page":"015003","DOI":"10.1088\/1478-3975\/ab5167","article-title":"Mapping spatio-temporal dynamics of single biomolecules in living cells","volume":"17","author":"Laurent","year":"2019","journal-title":"Phys. Biol"},{"key":"2023041403075540300_","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1038\/nmeth.1176","article-title":"High-density mapping of single-molecule trajectories with photoactivated localization microscopy","volume":"5","author":"Manley","year":"2008","journal-title":"Nat. Methods"},{"key":"2023041403075540300_","doi-asserted-by":"crossref","DOI":"10.1109\/ICASSP40776.2020.9054576","article-title":"Dense mapping of intracellular diffusion and drift from single-particle tracking data analysis","author":"Salomon","year":"2020"},{"key":"2023041403075540300_","doi-asserted-by":"crossref","first-page":"3783","DOI":"10.1038\/s41598-020-60220-1","article-title":"Statistical tests for force inference in heterogeneous environments","volume":"10","author":"Serov","year":"2020","journal-title":"Sci. Rep"},{"key":"2023041403075540300_","doi-asserted-by":"crossref","first-page":"2021","DOI":"10.1016\/j.bpj.2017.04.027","article-title":"An introduction to infinite HMMs for single-molecule data analysis","volume":"112","author":"Sgouralis","year":"2017","journal-title":"Biophys. J"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btac291\/43590044\/btac291.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/11\/3149\/49878590\/btac291.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/11\/3149\/49878590\/btac291.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,11,20]],"date-time":"2023-11-20T15:37:34Z","timestamp":1700494654000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/38\/11\/3149\/6575428"}},"subtitle":[],"editor":[{"given":"Janet","family":"Kelso","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2022,4,28]]},"references-count":15,"journal-issue":{"issue":"11","published-print":{"date-parts":[[2022,5,26]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btac291","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2022,6,1]]},"published":{"date-parts":[[2022,4,28]]}}}