{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,12]],"date-time":"2026-04-12T17:27:08Z","timestamp":1776014828638,"version":"3.50.1"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1009667","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2023,1,23]],"date-time":"2023-01-23T00:00:00Z","timestamp":1674432000000}}],"reference-count":52,"publisher":"Public Library of Science (PLoS)","issue":"12","license":[{"start":{"date-parts":[[2022,12,30]],"date-time":"2022-12-30T00:00:00Z","timestamp":1672358400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["R35GM136428"],"award-info":[{"award-number":["R35GM136428"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]},{"name":"National Cancer Institute","award":["R01CA252826"],"award-info":[{"award-number":["R01CA252826"]}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>\n                    We present an application of nonlinear image registration to align in microscopy time lapse sequences for every frame the cell outline and interior with the outline and interior of the same cell in a reference frame. The registration relies on a subcellular fiducial marker, a cell motion mask, and a topological regularization that enforces diffeomorphism on the registration without significant loss of granularity. This allows spatiotemporal analysis of extremely noisy and diffuse molecular processes across the entire cell. We validate the registration method for different fiducial markers by measuring the intensity differences between predicted and original time lapse sequences of Actin cytoskeleton images and by uncovering zones of spatially organized GEF- and GTPase signaling dynamics visualized by FRET-based activity biosensors in MDA-MB-231 cells. We then demonstrate applications of the registration method in conjunction with stochastic time-series analysis. We describe distinct zones of locally coherent dynamics of the cytoplasmic protein Profilin in U2OS cells. Further analysis of the Profilin dynamics revealed strong relationships with Actin cytoskeleton reorganization during cell symmetry-breaking and polarization. This study thus provides a framework for extracting information to explore functional interactions between cell morphodynamics, protein distributions, and signaling in cells undergoing continuous shape changes. Matlab code implementing the proposed registration method is available at\n                    <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/github.com\/DanuserLab\/Mask-Regularized-Diffeomorphic-Cell-Registration\" xlink:type=\"simple\">https:\/\/github.com\/DanuserLab\/Mask-Regularized-Diffeomorphic-Cell-Registration<\/jats:ext-link>\n                    .\n                  <\/jats:p>","DOI":"10.1371\/journal.pcbi.1009667","type":"journal-article","created":{"date-parts":[[2022,12,30]],"date-time":"2022-12-30T14:11:30Z","timestamp":1672409490000},"page":"e1009667","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":8,"title":["Fine-grained, nonlinear registration of live cell movies reveals spatiotemporal organization of diffuse molecular processes"],"prefix":"10.1371","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0086-5325","authenticated-orcid":true,"given":"Xuexia","family":"Jiang","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0511-0156","authenticated-orcid":true,"given":"Tadamoto","family":"Isogai","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2126-7751","authenticated-orcid":true,"given":"Joseph","family":"Chi","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8583-2014","authenticated-orcid":true,"given":"Gaudenz","family":"Danuser","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2022,12,30]]},"reference":[{"issue":"7260","key":"pcbi.1009667.ref001","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1038\/nature08242","article-title":"Coordination of Rho GTPase activities during cell protrusion","volume":"461","author":"M Machacek","year":"2009","journal-title":"Nature"},{"issue":"9","key":"pcbi.1009667.ref002","doi-asserted-by":"crossref","first-page":"3077","DOI":"10.1083\/jcb.201812073","article-title":"Spatiotemporal dynamics of GEF-H1 activation controlled by microtubule- and Src-mediated pathways","volume":"218","author":"ML Azoitei","year":"2019","journal-title":"J Cell Biol"},{"issue":"2","key":"pcbi.1009667.ref003","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1038\/ncb3292","article-title":"Locally excitable Cdc42 signals steer cells during chemotaxis","volume":"18","author":"HW Yang","year":"2016","journal-title":"Nat Cell Biol"},{"issue":"1","key":"pcbi.1009667.ref004","doi-asserted-by":"crossref","first-page":"188","DOI":"10.1016\/j.cell.2017.07.051","article-title":"Load Adaptation of Lamellipodial Actin Networks","volume":"171","author":"J Mueller","year":"2017","journal-title":"Cell"},{"issue":"5","key":"pcbi.1009667.ref005","doi-asserted-by":"crossref","first-page":"699","DOI":"10.1016\/j.devcel.2007.03.014","article-title":"GEF-H1 modulates localized RhoA activation during cytokinesis under the control of mitotic kinases","volume":"12","author":"J Birkenfeld","year":"2007","journal-title":"Dev Cell"},{"key":"pcbi.1009667.ref006","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1007\/978-1-4939-3542-0_4","article-title":"Measuring the Effects of Microtubule-Associated Proteins on Microtubule Dynamics In Vitro","volume":"1413","author":"M. Zanic","year":"2016","journal-title":"Methods Mol Biol"},{"issue":"Pt 24","key":"pcbi.1009667.ref007","doi-asserted-by":"crossref","first-page":"4201","DOI":"10.1242\/jcs.075150","article-title":"Micropatterning as a tool to decipher cell morphogenesis and functions","volume":"123","author":"M. Th\u00e9ry","year":"2010","journal-title":"J Cell Sci"},{"issue":"8","key":"pcbi.1009667.ref008","doi-asserted-by":"crossref","first-page":"e1006321","DOI":"10.1371\/journal.pcbi.1006321","article-title":"Profiling cellular morphodynamics by spatiotemporal spectrum decomposition","volume":"14","author":"X Ma","year":"2018","journal-title":"PLoS Comput Biol"},{"issue":"4","key":"pcbi.1009667.ref009","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1007\/s10059-010-0053-8","article-title":"Regulation of actin cytoskeleton dynamics in cells","volume":"29","author":"SH Lee","year":"2010","journal-title":"Mol Cells"},{"issue":"12","key":"pcbi.1009667.ref010","doi-asserted-by":"crossref","first-page":"2389","DOI":"10.1016\/j.bbamcr.2017.09.015","article-title":"Cell micropatterning reveals the modulatory effect of cell shape on proliferation through intracellular calcium transients","volume":"1864","author":"J Tong","year":"2017","journal-title":"Biochim Biophys Acta Mol Cell Res"},{"issue":"424","key":"pcbi.1009667.ref011","doi-asserted-by":"crossref","first-page":"rs3","DOI":"10.1126\/scisignal.aad4149","article-title":"Computational spatiotemporal analysis identifies WAVE2 and cofilin as joint regulators of costimulation-mediated T cell actin dynamics","volume":"9","author":"KT Roybal","year":"2016","journal-title":"Sci Signal"},{"issue":"4","key":"pcbi.1009667.ref012","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1109\/MSP.2017.2695801","article-title":"Optimal Mass Transport: Signal processing and machine-learning applications","volume":"34","author":"S Kolouri","year":"2017","journal-title":"IEEE Signal Process Mag"},{"issue":"3","key":"pcbi.1009667.ref013","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1023\/B:VISI.0000036836.66311.97","article-title":"Optimal Mass Transport for Registration and Warping","volume":"60","author":"S Haker","year":"2004","journal-title":"International Journal of Computer Vision"},{"issue":"1","key":"pcbi.1009667.ref014","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1016\/0004-3702(81)90024-2","article-title":"Determining optical flow","volume":"17","author":"BKP Horn","year":"1981","journal-title":"Artificial Intelligence"},{"key":"pcbi.1009667.ref015","author":"B Lucas","year":"1981","journal-title":"An Iterative Image Registration Technique with an Application to Stereo Vision (IJCAI)"},{"issue":"3","key":"pcbi.1009667.ref016","doi-asserted-by":"crossref","first-page":"433","DOI":"10.1145\/212094.212141","article-title":"The computation of optical flow","volume":"27","author":"SS Beauchemin","year":"1995","journal-title":"ACM Comput Surv"},{"issue":"4","key":"pcbi.1009667.ref017","doi-asserted-by":"crossref","first-page":"427","DOI":"10.1109\/TMI.2007.892508","article-title":"Brain functional localization: a survey of image registration techniques","volume":"26","author":"A Gholipour","year":"2007","journal-title":"IEEE Trans Med Imaging"},{"issue":"3","key":"pcbi.1009667.ref018","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1007\/s42452-021-04227-x","article-title":"Traditional and modern strategies for optical flow: an investigation","volume":"3","author":"STH Shah","year":"2021","journal-title":"SN Applied Sciences"},{"key":"pcbi.1009667.ref019","first-page":"356","volume-title":"European conference on computer vision; Florence","author":"P Kr\u00e4henb\u00fchl","year":"2012"},{"issue":"3","key":"pcbi.1009667.ref020","doi-asserted-by":"crossref","first-page":"274","DOI":"10.2174\/1573405612666160920123955","article-title":"A Review on Medical Image Registration as an Optimization Problem","volume":"13","author":"G Song","year":"2017","journal-title":"Curr Med Imaging Rev"},{"issue":"1","key":"pcbi.1009667.ref021","doi-asserted-by":"crossref","first-page":"S61","DOI":"10.1016\/j.neuroimage.2008.10.040","article-title":"Diffeomorphic demons: efficient non-parametric image registration","volume":"45","author":"T Vercauteren","year":"2009","journal-title":"Neuroimage"},{"issue":"12","key":"pcbi.1009667.ref022","doi-asserted-by":"crossref","first-page":"2887","DOI":"10.1088\/0031-9155\/50\/12\/011","article-title":"Validation of an accelerated \u2019demons\u2019 algorithm for deformable image registration in radiation therapy","volume":"50","author":"H Wang","year":"2005","journal-title":"Phys Med Biol"},{"issue":"9","key":"pcbi.1009667.ref023","doi-asserted-by":"crossref","first-page":"2165","DOI":"10.1109\/TMI.2019.2897112","article-title":"Learning a Probabilistic Model for Diffeomorphic Registration","volume":"38","author":"J Krebs","year":"2019","journal-title":"IEEE Trans Med Imaging"},{"key":"pcbi.1009667.ref024","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.50963","article-title":"Profilin and formin constitute a pacemaker system for robust actin filament growth","volume":"8","author":"J Funk","year":"2019","journal-title":"Elife"},{"issue":"1","key":"pcbi.1009667.ref025","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1016\/j.devcel.2014.10.027","article-title":"Profilin Regulates F-Actin Network Homeostasis by Favoring Formin over Arp2\/3 Complex","volume":"32","author":"C Suarez","year":"2015","journal-title":"Developmental Cell"},{"issue":"1","key":"pcbi.1009667.ref026","doi-asserted-by":"crossref","first-page":"54","DOI":"10.1016\/j.devcel.2014.10.026","article-title":"Profilin-1 Serves as a Gatekeeper for Actin Assembly by Arp2\/3-Dependent and -Independent Pathways","volume":"32","author":"D Rotty Jeremy","year":"2015","journal-title":"Developmental Cell"},{"key":"pcbi.1009667.ref027","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.55351","article-title":"Loss of Ena\/VASP interferes with lamellipodium architecture, motility and integrin-dependent adhesion","volume":"9","author":"J Damiano-Guercio","year":"2020","journal-title":"Elife"},{"issue":"5691","key":"pcbi.1009667.ref028","doi-asserted-by":"crossref","first-page":"1782","DOI":"10.1126\/science.1100533","article-title":"Two distinct actin networks drive the protrusion of migrating cells","volume":"305","author":"A Ponti","year":"2004","journal-title":"Science"},{"issue":"6","key":"pcbi.1009667.ref029","doi-asserted-by":"crossref","first-page":"471","DOI":"10.1016\/j.cels.2022.05.003","article-title":"Granger-causal inference of the lamellipodial actin regulator hierarchy by live cell imaging without perturbation","volume":"13","author":"J Noh","year":"2022","journal-title":"Cell Syst"},{"key":"pcbi.1009667.ref030","doi-asserted-by":"crossref","first-page":"21901","DOI":"10.1038\/srep21901","article-title":"Spatio-temporal co-ordination of RhoA, Rac1 and Cdc42 activation during prototypical edge protrusion and retraction dynamics","volume":"6","author":"K Martin","year":"2016","journal-title":"Sci Rep"},{"issue":"12","key":"pcbi.1009667.ref031","doi-asserted-by":"crossref","first-page":"1393","DOI":"10.1038\/ncb1797","article-title":"Fluctuations of intracellular forces during cell protrusion","volume":"10","author":"L Ji","year":"2008","journal-title":"Nat Cell Biol"},{"issue":"1","key":"pcbi.1009667.ref032","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1016\/j.cels.2015.07.001","article-title":"Functional hierarchy of redundant actin assembly factors revealed by fine-grained registration of intrinsic image fluctuations","volume":"1","author":"K Lee","year":"2015","journal-title":"Cell Syst"},{"issue":"377","key":"pcbi.1009667.ref033","doi-asserted-by":"crossref","first-page":"ra47","DOI":"10.1126\/scisignal.aaa8859","article-title":"ERK reinforces actin polymerization to power persistent edge protrusion during motility","volume":"8","author":"MC Mendoza","year":"2015","journal-title":"Sci Signal"},{"issue":"8","key":"pcbi.1009667.ref034","doi-asserted-by":"crossref","first-page":"826","DOI":"10.1038\/s41589-020-0542-9","article-title":"Multiplexed GTPase and GEF biosensor imaging enables network connectivity analysis","volume":"16","author":"DJ Marston","year":"2020","journal-title":"Nat Chem Biol"},{"key":"pcbi.1009667.ref035","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1016\/j.ymeth.2018.01.023","article-title":"Scanning fluorescence correlation spectroscopy comes full circle","volume":"140\u2013141","author":"G Gunther","year":"2018","journal-title":"Methods"},{"issue":"4","key":"pcbi.1009667.ref036","doi-asserted-by":"crossref","first-page":"498","DOI":"10.1038\/s41556-020-0488-x","article-title":"Systems analysis of RhoGEF and RhoGAP regulatory proteins reveals spatially organized RAC1 signalling from integrin adhesions","volume":"22","author":"PM M\u00fcller","year":"2020","journal-title":"Nat Cell Biol"},{"key":"pcbi.1009667.ref037","doi-asserted-by":"crossref","first-page":"545","DOI":"10.1146\/annurev.biophys.29.1.545","article-title":"Molecular mechanisms controlling actin filament dynamics in nonmuscle cells","volume":"29","author":"TD Pollard","year":"2000","journal-title":"Annu Rev Biophys Biomol Struct"},{"issue":"22","key":"pcbi.1009667.ref038","doi-asserted-by":"crossref","first-page":"3535","DOI":"10.1016\/j.cub.2017.10.002","article-title":"Profilin Directly Promotes Microtubule Growth through Residues Mutated in Amyotrophic Lateral Sclerosis","volume":"27","author":"JL Henty-Ridilla","year":"2017","journal-title":"Curr Biol"},{"issue":"11","key":"pcbi.1009667.ref039","doi-asserted-by":"crossref","first-page":"1435","DOI":"10.1038\/ncb3246","article-title":"Competition for actin between two distinct F-actin networks defines a bistable switch for cell polarization","volume":"17","author":"AJ Lomakin","year":"2015","journal-title":"Nat Cell Biol"},{"issue":"10","key":"pcbi.1009667.ref040","doi-asserted-by":"crossref","first-page":"851","DOI":"10.4169\/000298910x523344","article-title":"The Gini Index and Measures of Inequality","volume":"117","author":"FA Farris","year":"2010","journal-title":"The American Mathematical Monthly"},{"key":"pcbi.1009667.ref041","doi-asserted-by":"crossref","first-page":"361","DOI":"10.1146\/annurev.biophys.35.040405.102114","article-title":"Quantitative fluorescent speckle microscopy of cytoskeleton dynamics","volume":"35","author":"G Danuser","year":"2006","journal-title":"Annu Rev Biophys Biomol Struct"},{"issue":"12","key":"pcbi.1009667.ref042","doi-asserted-by":"crossref","first-page":"749","DOI":"10.1016\/j.tcb.2015.09.010","article-title":"Quantifying Modes of 3D Cell Migration","volume":"25","author":"MK Driscoll","year":"2015","journal-title":"Trends Cell Biol"},{"issue":"6386","key":"pcbi.1009667.ref043","article-title":"Observing the cell in its native state: Imaging subcellular dynamics in multicellular organisms","volume":"360","author":"TL Liu","year":"2018","journal-title":"Science"},{"issue":"9","key":"pcbi.1009667.ref044","doi-asserted-by":"crossref","first-page":"2025","DOI":"10.1038\/s41596-022-00706-6","article-title":"Isotropic imaging across spatial scales with axially swept light-sheet microscopy","volume":"17","author":"KM Dean","year":"2022","journal-title":"Nat Protoc"},{"issue":"W1","key":"pcbi.1009667.ref045","doi-asserted-by":"crossref","first-page":"W242","DOI":"10.1093\/nar\/gky354","article-title":"CRISPOR: intuitive guide selection for CRISPR\/Cas9 genome editing experiments and screens","volume":"46","author":"JP Concordet","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1009667.ref046","doi-asserted-by":"crossref","first-page":"10237","DOI":"10.1038\/ncomms10237","article-title":"A generic strategy for CRISPR-Cas9-mediated gene tagging","volume":"6","author":"DH Lackner","year":"2015","journal-title":"Nat Commun"},{"key":"pcbi.1009667.ref047","first-page":"756718","article-title":"Direct Arp2\/3-vinculin binding is essential for cell spreading, but only on compliant substrates and in 3D","author":"T Isogai","year":"2019","journal-title":"bioRxiv"},{"issue":"3","key":"pcbi.1009667.ref048","doi-asserted-by":"crossref","first-page":"444","DOI":"10.1016\/j.devcel.2019.04.007","article-title":"Enhanced Dendritic Actin Network Formation in Extended Lamellipodia Drives Proliferation in Growth-Challenged Rac1(P29S) Melanoma Cells","volume":"49","author":"AS Mohan","year":"2019","journal-title":"Dev Cell"},{"issue":"16","key":"pcbi.1009667.ref049","doi-asserted-by":"crossref","first-page":"5247","DOI":"10.1046\/j.1432-1327.2000.01600.x","article-title":"Functional characterization of green fluorescent protein\u2013profilin fusion proteins","volume":"267","author":"N Wittenmayer","year":"2000","journal-title":"European Journal of Biochemistry"},{"key":"pcbi.1009667.ref050","article-title":"Functional fluorescently-tagged human profilin","author":"ML Pimm","year":"2021","journal-title":"bioRxiv"},{"issue":"4","key":"pcbi.1009667.ref051","doi-asserted-by":"crossref","first-page":"2088","DOI":"10.1074\/jbc.M807073200","article-title":"Incompatibility with Formin Cdc12p Prevents Human Profilin from Substituting for Fission Yeast Profilin: Insights from Crystal Structures of Fission Yeast Profilin","volume":"284","author":"OC Ezezika","year":"2009","journal-title":"Journal of Biological Chemistry"},{"issue":"6","key":"pcbi.1009667.ref052","doi-asserted-by":"crossref","first-page":"1456","DOI":"10.1016\/j.bpj.2016.01.029","article-title":"Diagonally Scanned Light-Sheet Microscopy for Fast Volumetric Imaging of Adherent Cells","volume":"110","author":"KM Dean","year":"2016","journal-title":"Biophys J"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1009667","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2023,1,23]],"date-time":"2023-01-23T00:00:00Z","timestamp":1674432000000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1009667","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,23]],"date-time":"2023-01-23T13:50:26Z","timestamp":1674481826000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1009667"}},"subtitle":[],"editor":[{"given":"Melissa L.","family":"Kemp","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2022,12,30]]},"references-count":52,"journal-issue":{"issue":"12","published-online":{"date-parts":[[2022,12,30]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1009667","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2021.11.22.469497","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,12,30]]}}}