{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,13]],"date-time":"2026-01-13T09:23:59Z","timestamp":1768296239006,"version":"3.49.0"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1013864","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2026,1,12]],"date-time":"2026-01-12T00:00:00Z","timestamp":1768176000000}}],"reference-count":13,"publisher":"Public Library of Science (PLoS)","issue":"1","license":[{"start":{"date-parts":[[2026,1,5]],"date-time":"2026-01-05T00:00:00Z","timestamp":1767571200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Warwick Systems Biology Doctoral Training Centre"},{"name":"Institute of Advanced Study, University of Warwick"},{"DOI":"10.13039\/501100001255","name":"Lister Institute of Preventive Medicine","doi-asserted-by":"publisher","award":["Research Prize 2013"],"award-info":[{"award-number":["Research Prize 2013"]}],"id":[{"id":"10.13039\/501100001255","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["224563\/Z\/21\/Z"],"award-info":[{"award-number":["224563\/Z\/21\/Z"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>Here we describe the development of ShapeSpaceExplorer, an interactive software for the extraction, visualisation and analysis of complex 2D shape series. We also demonstrate its application to the analysis of cell morphology changes during cell migration. Cell migration is essential for many physiological and pathological processes. Intracellular force generation and transmission of these forces to extracellular structures or neighbouring cells drives cell migration. The emergent property of the processes driving cell migration is a change in cell shape. We describe a machine learning approach to understand the relationship of cell shape dynamics and cell migration behaviour. Our algorithm analyses cell shape from time-lapse images and learns the intrinsic low-dimensional structure of cell shape space. We use the resultant shape space map to visualise differences in cell shape distribution following perturbation experiments and to analyse the quantitative relationships between shape and migration behaviour. The core of our algorithm is a new, rapid, and landmark-free shape difference measure that allows unbiased analysis of the widely varying morphologies exhibited by migrating mesenchymal cells. We used our method to predict cell turning from dynamic cell shape information. ShapeSpaceExplorer can be applied widely to visualise and analyse cell morphology changes during development, the cell cycle and stress response, but also to the outlines of clusters, tissues and inanimate objects.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1013864","type":"journal-article","created":{"date-parts":[[2026,1,5]],"date-time":"2026-01-05T19:45:52Z","timestamp":1767642352000},"page":"e1013864","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["ShapeSpaceExplorer: Analysis of morphological transitions in migrating cells using similarity-based shape space mapping"],"prefix":"10.1371","volume":"22","author":[{"given":"Samuel D. R.","family":"Jefferyes","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Roswitha","family":"Gostner","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Laura","family":"Cooper","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mohammed M.","family":"Abdelsamea","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Elly","family":"Straube","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nasir","family":"Rajpoot","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8634-7168","authenticated-orcid":true,"given":"David B. A.","family":"Epstein","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2067-9041","authenticated-orcid":true,"given":"Anne","family":"Straube","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2026,1,5]]},"reference":[{"issue":"7248","key":"pcbi.1013864.ref001","doi-asserted-by":"crossref","first-page":"857","DOI":"10.1038\/nature08074","article-title":"A spatial gradient coordinates cell size and mitotic entry in fission yeast","volume":"459","author":"JB Moseley","year":"2009","journal-title":"Nature."},{"issue":"6","key":"pcbi.1013864.ref002","doi-asserted-by":"crossref","first-page":"1153","DOI":"10.1016\/j.devcel.2012.11.005","article-title":"Directional persistence of migrating cells requires Kif1C-mediated stabilization of trailing adhesions","volume":"23","author":"U Theisen","year":"2012","journal-title":"Dev Cell."},{"issue":"5832","key":"pcbi.1013864.ref003","doi-asserted-by":"crossref","first-page":"1753","DOI":"10.1126\/science.1140324","article-title":"Quantitative morphological signatures define local signaling networks regulating cell morphology","volume":"316","author":"C Bakal","year":"2007","journal-title":"Science."},{"issue":"35","key":"pcbi.1013864.ref004","doi-asserted-by":"crossref","first-page":"13978","DOI":"10.1073\/pnas.1201882109","article-title":"Super-resolution fluorescence imaging of organelles in live cells with photoswitchable membrane probes","volume":"109","author":"S-H Shim","year":"2012","journal-title":"Proc Natl Acad Sci U S A."},{"issue":"7194","key":"pcbi.1013864.ref005","doi-asserted-by":"crossref","first-page":"475","DOI":"10.1038\/nature06952","article-title":"Mechanism of shape determination in motile cells","volume":"453","author":"K Keren","year":"2008","journal-title":"Nature."},{"issue":"1","key":"pcbi.1013864.ref006","doi-asserted-by":"crossref","first-page":"6072","DOI":"10.1038\/s41598-020-62997-7","article-title":"Dynamic spherical harmonics approach for shape classification of migrating cells","volume":"10","author":"A Medyukhina","year":"2020","journal-title":"Sci Rep."},{"issue":"1","key":"pcbi.1013864.ref007","doi-asserted-by":"crossref","first-page":"11006","DOI":"10.1038\/s41598-023-35827-9","article-title":"Morphomigrational description as a new approach connecting cell\u2019s migration with its morphology","volume":"13","author":"T Ko\u0142odziej","year":"2023","journal-title":"Sci Rep."},{"key":"pcbi.1013864.ref008","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1016\/j.cag.2021.04.037","article-title":"InShaDe: invariant shape descriptors for visual 2D and 3D cellular and nuclear shape analysis and classification","volume":"98","author":"K Al-Thelaya","year":"2021","journal-title":"Computers & Graphics."},{"issue":"6","key":"pcbi.1013864.ref009","doi-asserted-by":"crossref","DOI":"10.1242\/dev.156778","article-title":"Morphometrics of complex cell shapes: lobe contribution elliptic Fourier analysis (LOCO-EFA)","volume":"145","author":"YE S\u00e1nchez-Corrales","year":"2018","journal-title":"Development."},{"issue":"1","key":"pcbi.1013864.ref010","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1016\/j.acha.2006.04.006","article-title":"Diffusion maps","volume":"21","author":"RR Coifman","year":"2006","journal-title":"Applied and Computational Harmonic Analysis."},{"issue":"5","key":"pcbi.1013864.ref011","doi-asserted-by":"crossref","first-page":"603","DOI":"10.1109\/34.1000236","article-title":"Mean shift: a robust approach toward feature space analysis","volume":"24","author":"D Comaniciu","year":"2002","journal-title":"IEEE Trans Pattern Anal Machine Intell."},{"key":"pcbi.1013864.ref012","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1007\/978-0-387-69935-6_13","volume-title":"Soft computing for knowledge discovery and data mining","author":"A Schclar","year":"2008"},{"key":"pcbi.1013864.ref013","first-page":"3463","article-title":"A novel framework for exploratory analysis of highly variable morphology of migrating epithelial cells","volume":"2013","author":"SDR Jefferyes","year":"2013","journal-title":"Annu Int Conf IEEE Eng Med Biol Soc."}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1013864","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2026,1,12]],"date-time":"2026-01-12T00:00:00Z","timestamp":1768176000000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1013864","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,12]],"date-time":"2026-01-12T18:50:59Z","timestamp":1768243859000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1013864"}},"subtitle":[],"editor":[{"given":"Jian","family":"Liu","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2026,1,5]]},"references-count":13,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,1,5]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1013864","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,1,5]]}}}