{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,17]],"date-time":"2026-10-17T15:07:03Z","timestamp":1792249623608,"version":"4.4.0"},"reference-count":32,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2025,9,1]],"date-time":"2025-09-01T00:00:00Z","timestamp":1756684800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2025,9,1]],"date-time":"2025-09-01T00:00:00Z","timestamp":1756684800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2025,6,30]],"date-time":"2025-06-30T00:00:00Z","timestamp":1751241600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000054","name":"National Institutes of Health National Cancer Institute","doi-asserted-by":"publisher","award":["R01 CA250636"],"award-info":[{"award-number":["R01 CA250636"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100005595","name":"University of California","doi-asserted-by":"publisher","award":["CRR-18-523872"],"award-info":[{"award-number":["CRR-18-523872"]}],"id":[{"id":"10.13039\/100005595","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010663","name":"European Research Council","doi-asserted-by":"publisher","award":["669941"],"award-info":[{"award-number":["669941"]}],"id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004412","name":"Human Frontier Science Program","doi-asserted-by":"publisher","award":["RGP0061 \/2015"],"award-info":[{"award-number":["RGP0061 \/2015"]}],"id":[{"id":"10.13039\/100004412","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000015","name":"US Department of Energy","doi-asserted-by":"publisher","award":["DE-SC0020338"],"award-info":[{"award-number":["DE-SC0020338"]}],"id":[{"id":"10.13039\/100000015","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000015","name":"US Department of Energy","doi-asserted-by":"publisher","award":["DE-SC0023184"],"award-info":[{"award-number":["DE-SC0023184"]}],"id":[{"id":"10.13039\/100000015","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100014807","name":"Cancer Research Coordinating Committee","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100014807","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000781","name":"European Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000781","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"NIH National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["R01 GM095904"],"award-info":[{"award-number":["R01 GM095904"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007185","name":"University of California, Los Angeles","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100007185","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010661","name":"Horizon 2020 Framework Programme","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100010661","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000854","name":"Human Frontier Science Program","doi-asserted-by":"publisher","award":["R01 CA250636"],"award-info":[{"award-number":["R01 CA250636"]}],"id":[{"id":"10.13039\/501100000854","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000854","name":"Human Frontier Science Program","doi-asserted-by":"publisher","award":["R01 GM095904"],"award-info":[{"award-number":["R01 GM095904"]}],"id":[{"id":"10.13039\/501100000854","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["SoftwareX"],"published-print":{"date-parts":[[2025,9]]},"DOI":"10.1016\/j.softx.2025.102255","type":"journal-article","created":{"date-parts":[[2025,7,22]],"date-time":"2025-07-22T08:58:09Z","timestamp":1753174689000},"page":"102255","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":6,"special_numbering":"C","title":["AlliGator: Open source fluorescence lifetime imaging analysis in G"],"prefix":"10.1016","volume":"31","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6602-7693","authenticated-orcid":false,"given":"Xavier","family":"Michalet","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"issue":"03","key":"10.1016\/j.softx.2025.102255_b1","doi-asserted-by":"crossref","DOI":"10.1117\/1.BIOS.2.3.030901","article-title":"High-speed fluorescence lifetime imaging microscopy: techniques, applications, and prospects","volume":"2","author":"Kanno","year":"2025","journal-title":"Biophotonics Discov"},{"issue":"6","key":"10.1016\/j.softx.2025.102255_b2","doi-asserted-by":"crossref","DOI":"10.1002\/jbio.202000472","article-title":"Mesoscopic fluorescence lifetime imaging: Fundamental principles, clinical applications and future directions","volume":"14","author":"Alfonso-Garcia","year":"2021","journal-title":"J Biophotonics"},{"issue":"6651","key":"10.1016\/j.softx.2025.102255_b3","doi-asserted-by":"crossref","first-page":"1270","DOI":"10.1126\/science.adf9725","article-title":"Wide-field fluorescence lifetime imaging of neuron spiking and subthreshold activity in vivo","volume":"380","author":"Bowman","year":"2023","journal-title":"Science"},{"issue":"3","key":"10.1016\/j.softx.2025.102255_b4","doi-asserted-by":"crossref","first-page":"618","DOI":"10.1158\/0008-5472.CAN-24-0880","article-title":"Fluorescence lifetime imaging enables in vivo quantification of PD-L1 expression and intertumoral heterogeneity","volume":"85","author":"Pal","year":"2025","journal-title":"Cancer Res"},{"key":"10.1016\/j.softx.2025.102255_b5","series-title":"Principles of fluorescence spectroscopy","author":"Lakowicz","year":"2006"},{"issue":"9","key":"10.1016\/j.softx.2025.102255_b6","doi-asserted-by":"crossref","first-page":"1979","DOI":"10.1038\/s41596-018-0026-5","article-title":"Fit-free analysis of fluorescence lifetime imaging data using the phasor approach","volume":"13","author":"Ranjit","year":"2018","journal-title":"Nat Protoc"},{"issue":"48","key":"10.1016\/j.softx.2025.102255_b7","doi-asserted-by":"crossref","first-page":"24019","DOI":"10.1073\/pnas.1912707116","article-title":"Fast fit-free analysis of fluorescence lifetime imaging via deep learning","volume":"116","author":"Smith","year":"2019","journal-title":"Proc Natl Acad Sci"},{"issue":"3","key":"10.1016\/j.softx.2025.102255_b8","doi-asserted-by":"crossref","DOI":"10.1002\/jbio.201800185","article-title":"In vitro and in vivo phasor analysis of stoichiometry and pharmacokinetics using short lifetime near-infrared dyes and time-gated imaging","volume":"12","author":"Chen","year":"2019","journal-title":"J Biophotonics"},{"issue":"2","key":"10.1016\/j.softx.2025.102255_b9","doi-asserted-by":"crossref","DOI":"10.1101\/2023.01.24.525411","article-title":"In vivo quantitative FRET small animal imaging : Intensity versus lifetime-based FRET","volume":"3","author":"Smith","year":"2023","journal-title":"Biophys Rep"},{"issue":"9","key":"10.1016\/j.softx.2025.102255_b10","doi-asserted-by":"crossref","first-page":"4637","DOI":"10.1364\/BOE.460216","article-title":"Design and characterization of a time-domain optical tomography platform for mesoscopic lifetime imaging","volume":"13","author":"Gao","year":"2022","journal-title":"Biomed Opt Express"},{"issue":"5","key":"10.1016\/j.softx.2025.102255_b11","doi-asserted-by":"crossref","first-page":"532","DOI":"10.1364\/OPTICA.454790","article-title":"In vitro and in vivo NIR fluorescence lifetime imaging with a time-gated SPAD camera","volume":"9","author":"Smith","year":"2022","journal-title":"Optica"},{"issue":"19","key":"10.1016\/j.softx.2025.102255_b12","doi-asserted-by":"crossref","first-page":"10104","DOI":"10.1021\/acsanm.5c01398","article-title":"Cyanine-conjugated gold nanospheres for near-infrared fluorescence-based biomedical imaging","volume":"8","author":"Chacko","year":"2025","journal-title":"ACS Appl Nano Mater"},{"issue":"1","key":"10.1016\/j.softx.2025.102255_b13","article-title":"Towards measurements of absolute membrane potential in Bacillus subtilis using fluorescence lifetime","volume":"5","author":"Roy","year":"2025","journal-title":"Biophys Rep"},{"issue":"2","key":"10.1016\/j.softx.2025.102255_b14","doi-asserted-by":"crossref","DOI":"10.1088\/2050-6120\/ab6ed7","article-title":"Wide-field time-gated SPAD imager for phasor-based FLIM applications","volume":"8","author":"Ulku","year":"2020","journal-title":"Methods Appl Fluoresc"},{"key":"10.1016\/j.softx.2025.102255_b15","series-title":"PhasorPy","year":"2025"},{"key":"10.1016\/j.softx.2025.102255_b16","series-title":"AlliGator Software Manual","author":"Michalet","year":"2025"},{"key":"10.1016\/j.softx.2025.102255_b17","series-title":"AlliGator Software Github Repository","author":"Michalet","year":"2025"},{"key":"10.1016\/j.softx.2025.102255_b18","series-title":"Data associated with \u201dAlliGator: Open Source Fluorescence Lifetime Imaging Analysis in G\u201d","author":"Michalet","year":"2025"},{"key":"10.1016\/j.softx.2025.102255_b19","series-title":"Medical image computing and computer assisted intervention","first-page":"265","article-title":"Cell detection with star-convex polygons","author":"Schmidt","year":"2018"},{"issue":"7","key":"10.1016\/j.softx.2025.102255_b20","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":"Nature Methods"},{"issue":"1","key":"10.1016\/j.softx.2025.102255_b21","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1021\/acsphotonics.9b00874","article-title":"Single-photon, time-gated, phasor-based fluorescence lifetime imaging through highly scattering medium","volume":"7","author":"Ankri","year":"2020","journal-title":"ACS Photonics"},{"issue":"22","key":"10.1016\/j.softx.2025.102255_b22","doi-asserted-by":"crossref","first-page":"6457","DOI":"10.1364\/OL.533923","article-title":"Deep learning-based temporal deconvolution for photon time-of-flight distribution retrieval","volume":"49","author":"Pandey","year":"2024","journal-title":"Opt Lett"},{"key":"10.1016\/j.softx.2025.102255_b23","series-title":"Sphinx","year":"2025"},{"key":"10.1016\/j.softx.2025.102255_b24","series-title":"ReadTheDocs","year":"2025"},{"key":"10.1016\/j.softx.2025.102255_b25","first-page":"123840P","article-title":"Near infrared fluorescence lifetime FRET microscopy to evaluate antibody drug binding in various HER2 positive cancer cell lines","volume":"12384","author":"Sherry","year":"2023","journal-title":"Proc SPIE"},{"key":"10.1016\/j.softx.2025.102255_b26","article-title":"Multiplexed fluorescence lifetime imaging of near-infrared fluorescent proteins in 3D tumor spheroids","volume":"12862","author":"Sherry","year":"2024","journal-title":"Proc SPIE"},{"key":"10.1016\/j.softx.2025.102255_b27","article-title":"Experimental study of fluorescence lifetime uncertainty in time-gated iccd-based macroscopic fluorescence lifetime imaging","author":"Yuan","year":"2024","journal-title":"Opt Biophotonics Congr: Biomed Opt"},{"key":"10.1016\/j.softx.2025.102255_b28","article-title":"Antibody-target binding quantification in living tumors using macroscopy fluorescence lifetime Forster resonance energy transfer imaging (MFLI FRET)","volume":"12821","author":"Yuan","year":"2024","journal-title":"Proc SPIE"},{"key":"10.1016\/j.softx.2025.102255_b29","series-title":"A novel technique for fluorescence lifetime tomography","author":"Nizam","year":"2025"},{"key":"10.1016\/j.softx.2025.102255_b30","series-title":"Real-time wide-field fluorescence lifetime imaging via single-snapshot acquisition for biomedical applications","author":"Pandey","year":"2025"},{"key":"10.1016\/j.softx.2025.102255_b31","doi-asserted-by":"crossref","DOI":"10.1002\/advs.202403253","article-title":"Fluorescence lifetime imaging for quantification of targeted drug delivery in varying tumor microenvironments","volume":"12","author":"Verma","year":"2025","journal-title":"Adv Sci"},{"key":"10.1016\/j.softx.2025.102255_b32","series-title":"AlliGator v1.01 Release","author":"Michalet","year":"2025"}],"container-title":["SoftwareX"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2352711025002225?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2352711025002225?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,5,15]],"date-time":"2026-05-15T21:04:55Z","timestamp":1778879095000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S2352711025002225"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,9]]},"references-count":32,"alternative-id":["S2352711025002225"],"URL":"https:\/\/doi.org\/10.1016\/j.softx.2025.102255","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2025.05.22.655640","asserted-by":"object"}]},"ISSN":["2352-7110"],"issn-type":[{"value":"2352-7110","type":"print"}],"subject":[],"published":{"date-parts":[[2025,9]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"AlliGator: Open source fluorescence lifetime imaging analysis in G","name":"articletitle","label":"Article Title"},{"value":"SoftwareX","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.softx.2025.102255","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"simple-article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2025 The Author. Published by Elsevier B.V.","name":"copyright","label":"Copyright"}],"article-number":"102255"}}