{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,20]],"date-time":"2026-10-20T00:22:00Z","timestamp":1792455720778,"version":"4.5.0"},"reference-count":36,"publisher":"Wiley","license":[{"start":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T00:00:00Z","timestamp":1791849600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"},{"start":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T00:00:00Z","timestamp":1791849600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"funder":[{"DOI":"10.13039\/100000923","name":"Silicon Valley Community Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000923","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Journal of Microscopy"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    Quantitative analysis of embryonic morphogenesis often requires handling terabyte\u2010scale 4D microscopy datasets, posing major computational and methodological challenges. Such analyses involve complex workflows for image restoration, segmentation, and tracking of thousands of cells in 3D, sometimes assembled from multiple generic tools and custom scripts. In their study\n                    <jats:italic>\u2018Deconstructing gastrulation at single\u2010cell resolution<\/jats:italic>\n                    ,\u2019 the authors present an integrated computational framework for cell segmentation, tracking and modelling of cell\u2013cell interactions during\n                    <jats:italic>Drosophila<\/jats:italic>\n                    gastrulation. Their approach combines both generic tools such as ilastik, FIJI, Cellpose, MATLAB code and tools such as ImSAnE to reconstruct whole\u2010embryo, single\u2010cell morphogenetic atlas with unprecedented detail. While the methodology is transparent and well\u2010documented, its implementation relies on multiple software environments and some non\u2013open\u2010source components, limiting full reproducibility and generalisability. Nevertheless, their \u2018computational framework\u2019 exemplifies rigorous data sharing, clear documentation, and methodological transparency aligned with several community guidelines for reproducible image analysis. We discuss this work in the context of reproducibility, replicability, generalisability, transparency, validity, and robustness, emphasising how emerging open\u2010source and popular solutions could improve accessibility and replicability of similar large\u2010scale bioimage analysis workflows in developmental biology.\n                  <\/jats:p>","DOI":"10.1111\/jmi.70132","type":"journal-article","created":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T15:17:16Z","timestamp":1791904636000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Reviewing reproducibility and replicability in \u2018Deconstructing gastrulation at single\u2010cell resolution\u2019 by Stern et\u00a0al. (2022)"],"prefix":"10.1111","author":[{"given":"Gabriel G","family":"Martins","sequence":"first","affiliation":[{"name":"GIMM \u2013 Gulbenkian Institute for Molecular Medicine  Oeiras Portugal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2180-2614","authenticated-orcid":false,"given":"Haydee O.","family":"Hern\u00e1ndez","sequence":"additional","affiliation":[{"name":"Centro de Investigaci\u00f3n en Ciencias Universidad Aut\u00f3noma del Estado de Morelos  Cuernavaca Morelos Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lachlan","family":"Whitehead","sequence":"additional","affiliation":[{"name":"Walter and Eliza Hall Institute of Medical Research  Parkville Victoria Australia"},{"name":"Department of Medical Biology University of Melbourne  Parkville Victoria Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pradeep","family":"Rajasekhar","sequence":"additional","affiliation":[{"name":"Walter and Eliza Hall Institute of Medical Research  Parkville Victoria Australia"},{"name":"Department of Medical Biology University of Melbourne  Parkville Victoria Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,10,13]]},"reference":[{"key":"e_1_2_8_2_1","doi-asserted-by":"crossref","first-page":"1861","DOI":"10.1016\/j.cub.2022.02.059","article-title":"Deconstructing gastrulation at single\u2010cell resolution","volume":"32","author":"Stern T.","year":"2022","journal-title":"Current Biology"},{"key":"e_1_2_8_3_1","doi-asserted-by":"crossref","first-page":"176","DOI":"10.1186\/s12859-019-2720-x","article-title":"3DMMS: Robust 3D membrane morphological segmentation of C. elegans embryo","volume":"20","author":"Cao J.","year":"2019","journal-title":"BMC 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