{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,8]],"date-time":"2026-07-08T13:30:08Z","timestamp":1783517408245,"version":"3.55.0"},"reference-count":19,"publisher":"Wiley","license":[{"start":{"date-parts":[[2026,7,8]],"date-time":"2026-07-08T00:00:00Z","timestamp":1783468800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,7,8]],"date-time":"2026-07-08T00:00:00Z","timestamp":1783468800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"funder":[{"DOI":"10.13039\/100020595","name":"National Science and Technology Council","doi-asserted-by":"publisher","award":["NSTC\u2010113\u20102320\u2010B\u2010002\u2010076"],"award-info":[{"award-number":["NSTC\u2010113\u20102320\u2010B\u2010002\u2010076"]}],"id":[{"id":"10.13039\/100020595","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>Image quantification is central to modern biomedical research. However, the reproducibility of image\u2010based studies remains a persistent challenge due to limited access to raw data and incomplete reporting of analysis workflows. To assess these issues, the Global Bioimage Analyst Society (GloBIAS) launched a coordinated effort in 2024 to examine published bioimage analysis workflows.<\/jats:p>\n                  <jats:p>\n                    Here, we evaluated the reproducibility of a published workflow for analysing cell shape transitions in\n                    <jats:italic>Dictyostelium discoideum<\/jats:italic>\n                    . While the reported kymographs and biological conclusions could be qualitatively reproduced, a critical upstream step \u2013 cell segmentation \u2013 was insufficiently described. Reproducing the segmentation step based on the available information required extensive parameter tuning and failed to consistently capture accurate cell contours, thereby compromising downstream analysis. To evaluate whether the downstream analytical components could be reproduced when segmentation quality was improved, we adopted an alternative segmentation strategy using ilastik, a machine learning\u2010based image analysis tool. Using cell\u2010boundary coordinates extracted from ilastik\u2010based masks as alternative inputs for downstream analysis, we reconstructed kymographs that partially matched the published results.\n                  <\/jats:p>\n                  <jats:p>Our findings demonstrate that accessible software and raw data alone are insufficient to ensure reproducibility in image\u2010based research. Complete reporting of image\u2010processing workflows, including segmentation strategies and parameter settings, is essential for the reliable reproduction of published quantitative analyses.<\/jats:p>","DOI":"10.1111\/jmi.70143","type":"journal-article","created":{"date-parts":[[2026,7,8]],"date-time":"2026-07-08T13:10:38Z","timestamp":1783516238000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Reproducibility assessment of a published cell shape transition analysis workflow"],"prefix":"10.1111","author":[{"given":"Esteban A.","family":"Miglietta","sequence":"first","affiliation":[{"name":"Cimini Lab Imaging Platform Broad Institute of MIT &amp; Harvard  Cambridge Massachusetts USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"An\u2010Chi","family":"Luo","sequence":"additional","affiliation":[{"name":"Imaging Core College of Medicine National Taiwan University  Taipei City Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Agustin A.","family":"Corbat","sequence":"additional","affiliation":[{"name":"Facultad de Ciencias Exactas y Naturales Instituto de F\u00edsica de Buenos Aires Universidad de Buenos Aires  Buenos Aires Argentina"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shao\u2010Chun","family":"Hsu","sequence":"additional","affiliation":[{"name":"Imaging Core College of Medicine National Taiwan University  Taipei City Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,7,8]]},"reference":[{"key":"e_1_2_7_2_1","doi-asserted-by":"crossref","DOI":"10.3389\/fcell.2022.898351","article-title":"Spontaneous transitions between amoeboid and keratocyte\u2010like modes of migration","volume":"10","author":"Moldenhawer T.","year":"2022","journal-title":"Frontiers in Cell and Developmental Biology"},{"key":"e_1_2_7_3_1","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.55133","article-title":"Imaging methods are vastly underreported in biomedical research","volume":"9","author":"Marqu\u00e9s G.","year":"2020","journal-title":"Elife"},{"issue":"3","key":"e_1_2_7_4_1","doi-asserted-by":"crossref","DOI":"10.15252\/embj.2020105889","article-title":"Reproducible image handling and analysis","volume":"40","author":"Miura K.","year":"2021","journal-title":"Embo Journal"},{"issue":"12","key":"e_1_2_7_5_1","doi-asserted-by":"crossref","first-page":"1423","DOI":"10.1038\/s41592-021-01162-y","article-title":"QUAREP\u2010LiMi: A community endeavor to advance quality assessment and reproducibility in light microscopy","volume":"18","author":"Boehm U.","year":"2021","journal-title":"Nature Methods"},{"issue":"2","key":"e_1_2_7_6_1","doi-asserted-by":"crossref","first-page":"170","DOI":"10.1038\/s41592-023-01987-9","article-title":"Community\u2010developed checklists for publishing images and image analyses","volume":"21","author":"Schmied C.","year":"2024","journal-title":"Nature Methods"},{"issue":"6","key":"e_1_2_7_7_1","doi-asserted-by":"crossref","first-page":"877","DOI":"10.1038\/s41556-025-01704-y","article-title":"Light microscopy reporting for reproducibility","volume":"27","year":"2025","journal-title":"Nature Cell Biology"},{"key":"e_1_2_7_8_1","doi-asserted-by":"crossref","unstructured":"Corbat A. A. Walther C. G. de laBallina L. R. Condon N. D. Felder A. A. Sch\u00e4tz M. Schmerl B. Sugawara K. Prats C. Klemm A. Miura K. Sampaio P. Tischer C. Levet F. D'Antuono R. Cimini B. A. &Haase R.(2026).GloBIAS: Strengthening the foundations of bioimage analysis.Nature Methods https:\/\/doi.org\/10.1038\/s41592-026-03060-7","DOI":"10.1038\/s41592-026-03060-7"},{"issue":"8","key":"e_1_2_7_9_1","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1009268","article-title":"Analysis of protrusion dynamics in amoeboid cell motility by means of regularized contour flows","volume":"17","author":"Schindler D.","year":"2021","journal-title":"PLOS Computational Biology"},{"key":"e_1_2_7_10_1","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1007\/978-1-0716-4023-4_13","article-title":"A hands\u2010on guide to AmoePy \u2013 A Python\u2010based software package to analyze cell migration data","volume":"2828","author":"Moldenhawer T.","year":"2024","journal-title":"Methods in Molecular Biology"},{"key":"e_1_2_7_11_1","unstructured":"Daniel Schindler T. Moldenhawer T. Lindenmeier L. Lesur V. &Holschneider M.(2025).AmoePy (1.10). Zenodo."},{"issue":"3","key":"e_1_2_7_12_1","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1109\/83.661186","article-title":"Snakes, shapes, and gradient vector flow","volume":"7","author":"Xu C.","year":"1998","journal-title":"IEEE Transactions on Image Processing"},{"issue":"5","key":"e_1_2_7_13_1","doi-asserted-by":"crossref","DOI":"10.1088\/1478-3975\/8\/5\/055001","article-title":"Local and global measures of shape dynamics","volume":"8","author":"Driscoll M.","year":"2011","journal-title":"Physical Biology"},{"issue":"4","key":"e_1_2_7_14_1","doi-asserted-by":"crossref","first-page":"1439","DOI":"10.1529\/biophysj.105.070383","article-title":"Morphodynamic profiling of protrusion phenotypes","volume":"90","author":"Machacek M.","year":"2006","journal-title":"Biophysical Journal"},{"issue":"7","key":"e_1_2_7_15_1","doi-asserted-by":"crossref","first-page":"518","DOI":"10.1002\/mrd.22489","article-title":"The ImageJ ecosystem: An open platform for biomedical image analysis","volume":"82","author":"Schindelin J.","year":"2015","journal-title":"Molecular Reproduction and Development"},{"issue":"1","key":"e_1_2_7_16_1","doi-asserted-by":"crossref","first-page":"529","DOI":"10.1186\/s12859-017-1934-z","article-title":"ImageJ2: ImageJ for the next generation of scientific image data","volume":"18","author":"Rueden C. T.","year":"2017","journal-title":"BMC Bioinformatics [Electronic Resource]"},{"issue":"4","key":"e_1_2_7_17_1","doi-asserted-by":"crossref","first-page":"1005","DOI":"10.1242\/jcs.106.4.1005","article-title":"The locomotion, shape and pseudopodial dynamics of unstimulated Dictyostelium cells are not random","volume":"106","author":"Killich T.","year":"1993","journal-title":"Journal of Cell Science"},{"key":"e_1_2_7_18_1","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0003734","article-title":"Ordered patterns of cell shape and orientational correlation during spontaneous cell migration","volume":"3","author":"Maeda Y. T.","year":"2008","journal-title":"PLoS ONE"},{"key":"e_1_2_7_19_1","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1002392","article-title":"Cell shape dynamics: From waves to migration","volume":"8","author":"Driscoll M. K.","year":"2012","journal-title":"PLOS Computational Biology"},{"issue":"12","key":"e_1_2_7_20_1","doi-asserted-by":"crossref","first-page":"1226","DOI":"10.1038\/s41592-019-0582-9","article-title":"ilastik: Interactive machine learning for (bio)image analysis","volume":"16","author":"Berg S.","year":"2019","journal-title":"Nature Methods"}],"container-title":["Journal of Microscopy"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/jmi.70143","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/full-xml\/10.1111\/jmi.70143","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/jmi.70143","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,8]],"date-time":"2026-07-08T13:10:41Z","timestamp":1783516241000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1111\/jmi.70143"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,7,8]]},"references-count":19,"alternative-id":["10.1111\/jmi.70143"],"URL":"https:\/\/doi.org\/10.1111\/jmi.70143","archive":["Portico"],"relation":{},"ISSN":["0022-2720","1365-2818"],"issn-type":[{"value":"0022-2720","type":"print"},{"value":"1365-2818","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,7,8]]},"assertion":[{"value":"2025-12-03","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-06-25","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-07-08","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"jmi.70143"}}