{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T11:52:22Z","timestamp":1791373942599,"version":"4.3.1"},"reference-count":0,"publisher":"The Company of Biologists","license":[{"start":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T00:00:00Z","timestamp":1791331200000},"content-version":"am","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"abstract":"<jats:p>Understanding development in living organisms requires following the divisions, movements, and fates of cells. While advances in microscopy have enabled whole-embryo imaging at the cellular level, extracting and analyzing cell lineages from these massive datasets remains a significant computational challenge. We present Mastodon, a scalable, extensible software platform for manual, semi-automated, and automated cell tracking in large images. A purpose-built graph model supports responsive performance for datasets with millions of annotations, making Mastodon a scalable platform for cell lineage analysis. Built as a Fiji plugin, Mastodon enables interactive visualization, editing, and analysis of complex lineage trees, seamlessly integrated with the raw image data. Comprehension of cell lineages in complex three-dimensional geometries is facilitated by interoperability with the powerful open-source render engine Blender. In three distinct developmental contexts, we demonstrate how Mastodon will accelerate biological insights by providing user-friendly navigation and explorative analysis in complex lineage datasets.<\/jats:p>","DOI":"10.1242\/dev.205569","type":"journal-article","created":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T11:13:19Z","timestamp":1791371599000},"source":"Crossref","is-referenced-by-count":0,"title":["Mastodon: the command center for large-scale lineage-tracing microscopy datasets"],"prefix":"10.1242","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9029-3625","authenticated-orcid":false,"given":"Johannes","family":"Girstmair","sequence":"first","affiliation":[{"name":"1 Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstra\u00dfe 108, 01307 Dresden, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9477-3957","authenticated-orcid":false,"given":"Tobias","family":"Pietzsch","sequence":"additional","affiliation":[{"name":"1 Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstra\u00dfe 108, 01307 Dresden, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4270-7982","authenticated-orcid":false,"given":"Vladimir","family":"Ulman","sequence":"additional","affiliation":[{"name":"1 Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstra\u00dfe 108, 01307 Dresden, Germany"},{"name":"3 Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czechia"},{"name":"4 IT4Innovations, VSB \u2013 Technical University of Ostrava, Ostrava, Czechia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8145-7090","authenticated-orcid":false,"given":"Stefan","family":"Hahmann","sequence":"additional","affiliation":[{"name":"2 Center for Scalable Data Analytics and Artificial Intelligence (ScaDS.AI), Dresden and Leipzig, Germany"},{"name":"8 DFG Cluster of Excellence Physics of Life (PoL) at the Technische Universit\u00e4t Dresden (TUD), Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-2769-1715","authenticated-orcid":false,"given":"Matthias","family":"Arzt","sequence":"additional","affiliation":[{"name":"1 Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstra\u00dfe 108, 01307 Dresden, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3908-7233","authenticated-orcid":false,"given":"Mette","family":"Handberg-Thorsager","sequence":"additional","affiliation":[{"name":"1 Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstra\u00dfe 108, 01307 Dresden, Germany"},{"name":"5 Georg-August-University Goettingen, Goettingen, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-1388-8959","authenticated-orcid":false,"given":"Samuel","family":"Pantze","sequence":"additional","affiliation":[{"name":"6 Center for Advanced Systems Understanding (CASUS), G\u00f6rlitz, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1392-9340","authenticated-orcid":false,"given":"Ko","family":"Sugawara","sequence":"additional","affiliation":[{"name":"7 RIKEN Center for Biosystems Dynamics Research, Kobe, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5949-2327","authenticated-orcid":false,"given":"Robert","family":"Haase","sequence":"additional","affiliation":[{"name":"2 Center for Scalable Data Analytics and Artificial Intelligence (ScaDS.AI), Dresden and Leipzig, Germany"},{"name":"8 DFG Cluster of Excellence Physics of Life (PoL) at the Technische Universit\u00e4t Dresden (TUD), Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8255-1724","authenticated-orcid":false,"given":"Shuichi","family":"Onami","sequence":"additional","affiliation":[{"name":"7 RIKEN Center for Biosystems Dynamics Research, Kobe, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0998-4718","authenticated-orcid":false,"given":"Jean-Yves","family":"Tinevez","sequence":"additional","affiliation":[{"name":"9 Institut Pasteur, Universit\u00e9 Paris Cit\u00e9, Image Analysis Hub, Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2222-9370","authenticated-orcid":false,"given":"Pavel","family":"Tomancak","sequence":"additional","affiliation":[{"name":"1 Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstra\u00dfe 108, 01307 Dresden, Germany"},{"name":"8 DFG Cluster of Excellence Physics of Life (PoL) at the Technische Universit\u00e4t Dresden (TUD), Germany"},{"name":"10 Center for Systems Biology Dresden, Dresden, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"237","published-online":{"date-parts":[[2026,10,7]]},"container-title":["Development"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.biologists.com\/dev\/article-pdf\/doi\/10.1242\/dev.205569\/3720408\/dev205569.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/journals.biologists.com\/dev\/article-pdf\/doi\/10.1242\/dev.205569\/3720408\/dev205569.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T11:13:19Z","timestamp":1791371599000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.biologists.com\/dev\/article\/doi\/10.1242\/dev.205569\/373101\/Mastodon-the-command-center-for-large-scale"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,10,7]]},"references-count":0,"URL":"https:\/\/doi.org\/10.1242\/dev.205569","relation":{},"ISSN":["0950-1991","1477-9129"],"issn-type":[{"value":"0950-1991","type":"print"},{"value":"1477-9129","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,10,7]]},"article-number":"dev.205569"}}