{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T14:00:06Z","timestamp":1785420006680,"version":"3.56.0"},"reference-count":43,"publisher":"eLife Sciences Publications, Ltd","license":[{"start":{"date-parts":[[2022,9,28]],"date-time":"2022-09-28T00:00:00Z","timestamp":1664323200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2022,9,28]],"date-time":"2022-09-28T00:00:00Z","timestamp":1664323200000},"content-version":"am","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2022,9,28]],"date-time":"2022-09-28T00:00:00Z","timestamp":1664323200000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100011033","name":"Agencia Estatal de Investigaci\u00f3n","doi-asserted-by":"publisher","award":["PGC2018-095663-B-I00"],"award-info":[{"award-number":["PGC2018-095663-B-I00"]}],"id":[{"id":"10.13039\/501100011033","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100011033","name":"Agencia Estatal de Investigaci\u00f3n","doi-asserted-by":"publisher","award":["PGC2018-101643-B-I00"],"award-info":[{"award-number":["PGC2018-101643-B-I00"]}],"id":[{"id":"10.13039\/501100011033","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100011033","name":"Agencia Estatal de Investigaci\u00f3n","doi-asserted-by":"publisher","award":["CEX2018-000792-M"],"award-info":[{"award-number":["CEX2018-000792-M"]}],"id":[{"id":"10.13039\/501100011033","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003741","name":"Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003741","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elifesciences.org"],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2022,9,27]]},"abstract":"<jats:p>\n                    Reconstruction of prototypic three-dimensional (3D) atlases at the scale of whole tissues or organs requires specific methods to be developed. We have established a digital 3D-atlas maker (DAMAKER) and built a digital 3D-atlas to monitor the changes in the growth of the neuronal differentiation domain in the zebrafish hindbrain upon time. DAMAKER integrates spatial and temporal data of cell populations, neuronal differentiation and brain morphogenesis, through\n                    <jats:italic>in vivo<\/jats:italic>\n                    imaging techniques paired with image analyses and segmentation tools. First, we generated a 3D-reference from several imaged hindbrains and segmented them using a trainable tool; these were aligned using rigid registration, revealing distribution of neuronal differentiation growth patterns along the axes. Second, we quantified the dynamic growth of the neuronal differentiation domain by\n                    <jats:italic>in vivo<\/jats:italic>\n                    neuronal birthdating experiments. We generated digital neuronal birthdating 3D-maps and revealed that the temporal order of neuronal differentiation prefigured the spatial distribution of neurons in the tissue, with an inner-outer differentiation gradient. Last, we applied it to specific differentiated neuronal populations such as glutamatergic and GABAergic neurons, as proof-of-concept that the digital birthdating 3D-maps could be used as a proxy to infer neuronal birthdate. As this protocol uses open-access tools and algorithms, it can be shared for standardized, accessible, tissue-wide cell population atlas construction.\n                  <\/jats:p>","DOI":"10.7554\/elife.78300","type":"journal-article","created":{"date-parts":[[2022,9,28]],"date-time":"2022-09-28T08:00:36Z","timestamp":1664352036000},"update-policy":"https:\/\/doi.org\/10.7554\/elife.78300","source":"Crossref","is-referenced-by-count":2,"title":["A dynamic and expandable digital 3D-atlas maker for monitoring the temporal changes in tissue growth during hindbrain morphogenesis"],"prefix":"10.7554","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4892-8161","authenticated-orcid":true,"given":"Matthias","family":"Blanc","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04n0g0b29","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Medicine and Life Sciences, Universitat Pompeu Fabra","place":["Barcelona, Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Giovanni","family":"Dalmasso","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/03mstc592","id-type":"ROR","asserted-by":"publisher"}],"name":"European Molecular Biology Laboratory","place":["Barcelona, Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7155-4153","authenticated-orcid":true,"given":"Frederic","family":"Udina","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04n0g0b29","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Economics and Business, Universitat Pompeu Fabra","place":["Barcelona, Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6423-7451","authenticated-orcid":true,"given":"Cristina","family":"Pujades","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04n0g0b29","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Medicine and Life Sciences, Universitat Pompeu Fabra","place":["Barcelona, Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"4374","published-online":{"date-parts":[[2022,9,28]]},"reference":[{"key":"bib1","doi-asserted-by":"publisher","first-page":"2424","DOI":"10.1093\/bioinformatics\/btx180","article-title":"Trainable weka segmentation: a machine learning tool for microscopy pixel classification","volume":"33","author":"Arganda-Carreras","year":"2017","journal-title":"Bioinformatics"},{"key":"bib2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0228225","article-title":"The interplay of Atoh1 genes in the lower rhombic lip during hindbrain morphogenesis","volume":"15","author":"Belzunce","year":"2020","journal-title":"PLOS ONE"},{"key":"bib3","article-title":"Cristinapujades","volume-title":"Software Heritage","author":"Blanc","year":"2022","unstructured":"Blanc M. 2022. 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