{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,9]],"date-time":"2026-09-09T03:40:13Z","timestamp":1788925213356,"version":"build-2803163510"},"reference-count":30,"publisher":"The Company of Biologists","issue":"6","license":[{"start":{"date-parts":[[2024,6,18]],"date-time":"2024-06-18T00:00:00Z","timestamp":1718668800000},"content-version":"vor","delay-in-days":3,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/501100004794","name":"Centre National de la Recherche Scientifique","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100004794","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100007586","name":"Aix-Marseille University","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100007586","id-type":"DOI","asserted-by":"crossref"}]},{"name":"European Research Council under the European Union's Horizon 2020 Programme","award":["ERC-2019-SyG 856118"],"award-info":[{"award-number":["ERC-2019-SyG 856118"]}]},{"name":"France-BioImaging national research infrastructure","award":["ANR-10-INBS-04-01"],"award-info":[{"award-number":["ANR-10-INBS-04-01"]}]},{"name":"France 2030","award":["ANR-16-CONV-0001"],"award-info":[{"award-number":["ANR-16-CONV-0001"]}]},{"name":"Excellence Initiative of Aix-Marseille University,"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,6,15]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n               <jats:p>Regular spatial patterns are ubiquitous forms of organization in nature. In animals, regular patterns can be found from the cellular scale to the tissue scale, and from early stages of development to adulthood. To understand the formation of these patterns, how they assemble and mature, and how they are affected by perturbations, a precise quantitative description of the patterns is essential. However, accessible tools that offer in-depth analysis without the need for computational skills are lacking for biologists. Here, we present PatternJ, a novel toolset to analyze regular one-dimensional patterns precisely and automatically. This toolset, to be used with the popular imaging processing program ImageJ\/Fiji, facilitates the extraction of key geometric features within and between pattern repeats in static images and time-lapse series. We validate PatternJ with simulated data and test it on images of sarcomeres from insect muscles and contracting cardiomyocytes, actin rings in neurons, and somites from zebrafish embryos obtained using confocal fluorescence microscopy, STORM, electron microscopy, and brightfield imaging. We show that the toolset delivers subpixel feature extraction reliably even with images of low signal-to-noise ratio. PatternJ's straightforward use and functionalities make it valuable for various scientific fields requiring quantitative one-dimensional pattern analysis, including the sarcomere biology of muscles or the patterning of mammalian axons, speeding up discoveries with the bonus of high reproducibility.<\/jats:p>","DOI":"10.1242\/bio.060548","type":"journal-article","created":{"date-parts":[[2024,6,18]],"date-time":"2024-06-18T08:14:26Z","timestamp":1718698466000},"source":"Crossref","is-referenced-by-count":13,"title":["PatternJ: an ImageJ toolset for the automated and quantitative analysis of regular spatial patterns found in sarcomeres, axons, somites, and more"],"prefix":"10.1242","volume":"13","author":[{"given":"M\u00e9lina","family":"Baheux Blin","sequence":"first","affiliation":[{"name":"Aix Marseille Universit\u00e9, CNRS, Institut de Biologie du D\u00e9veloppement de Marseille, IBDM-UMR7288 , Marseille 13009 , France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0556-2825","authenticated-orcid":false,"given":"Vincent","family":"Loreau","sequence":"additional","affiliation":[{"name":"Aix Marseille Universit\u00e9, CNRS, Institut de Biologie du D\u00e9veloppement de Marseille, IBDM-UMR7288 , Marseille 13009 , France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9518-7263","authenticated-orcid":false,"given":"Frank","family":"Schnorrer","sequence":"additional","affiliation":[{"name":"Aix Marseille Universit\u00e9, CNRS, Institut de Biologie du D\u00e9veloppement de Marseille, IBDM-UMR7288 , Marseille 13009 , France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8305-7322","authenticated-orcid":false,"given":"Pierre","family":"Mangeol","sequence":"additional","affiliation":[{"name":"Aix Marseille Universit\u00e9, CNRS, Institut de Biologie du D\u00e9veloppement de Marseille, IBDM-UMR7288 , Marseille 13009 , France"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"237","published-online":{"date-parts":[[2024,6,18]]},"reference":[{"key":"2024061808140219000_BIO060548C1","doi-asserted-by":"publisher","first-page":"813","DOI":"10.1387\/ijdb.072556cc","article-title":"Reptile scale paradigm: Evo-Devo, pattern formation and regeneration","volume":"53","author":"Chang","year":"2009","journal-title":"Int. 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