{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,24]],"date-time":"2026-02-24T17:40:31Z","timestamp":1771954831607,"version":"3.50.1"},"reference-count":8,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2023,7,12]],"date-time":"2023-07-12T00:00:00Z","timestamp":1689120000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2023,7,12]],"date-time":"2023-07-12T00:00:00Z","timestamp":1689120000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                <jats:title>Motivation<\/jats:title>\n                <jats:p>Quantitative descriptions of multi-cellular structures from optical microscopy imaging are prime to understand the variety of three-dimensional (3D) shapes in living organisms. Experimental models of vertebrates, invertebrates and plants, such as zebrafish, killifish, <jats:italic>Drosophila<\/jats:italic> or <jats:italic>Marchantia<\/jats:italic>, mainly comprise multilayer tissues, and even if microscopes can reach the needed depth, their geometry hinders the selection and subsequent analysis of the optical volumes of interest. Computational tools to \u201cpeel\u201d tissues by removing specific layers and reducing 3D volume into planar images, can critically improve visualization and analysis.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>We developed VolumePeeler, a versatile FIJI plugin for virtual 3D \u201cpeeling\u201d of image stacks. The plugin implements spherical and spline surface projections. We applied VolumePeeler to perform peeling in 3D images of spherical embryos, as well as non-spherical tissue layers. The produced images improve the 3D volume visualization and enable analysis and quantification of geometrically challenging microscopy datasets.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Availability<\/jats:title>\n                <jats:p>ImageJ\/FIJI software, source code, examples, and tutorials are openly available in <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/cimt.uchile.cl\/mcerda\">https:\/\/cimt.uchile.cl\/mcerda<\/jats:ext-link><\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12859-023-05403-z","type":"journal-article","created":{"date-parts":[[2023,7,12]],"date-time":"2023-07-12T10:02:08Z","timestamp":1689156128000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["VolumePeeler: a novel FIJI plugin for geometric tissue peeling to improve visualization and quantification of 3D image stacks"],"prefix":"10.1186","volume":"24","author":[{"given":"Marilyn","family":"Gatica","sequence":"first","affiliation":[]},{"given":"Carlos F.","family":"Navarro","sequence":"additional","affiliation":[]},{"given":"Alejandro","family":"Lavado","sequence":"additional","affiliation":[]},{"given":"German","family":"Reig","sequence":"additional","affiliation":[]},{"given":"Eduardo","family":"Pulgar","sequence":"additional","affiliation":[]},{"given":"Paula","family":"Llanos","sequence":"additional","affiliation":[]},{"given":"Steffen","family":"H\u00e4rtel","sequence":"additional","affiliation":[]},{"given":"Andrea","family":"Ravasio","sequence":"additional","affiliation":[]},{"given":"Cristina","family":"Bertocchi","sequence":"additional","affiliation":[]},{"given":"Miguel L.","family":"Concha","sequence":"additional","affiliation":[]},{"given":"Mauricio","family":"Cerda","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2023,7,12]]},"reference":[{"issue":"1","key":"5403_CR1","doi-asserted-by":"publisher","first-page":"2207","DOI":"10.1038\/ncomms3207","volume":"4","author":"B Schmid","year":"2013","unstructured":"Schmid B, Shah G, Scherf N, Weber M, Thierbach K, Campos CP, Roeder I, Aanstad P, Huisken J. High-speed panoramic light-sheet microscopy reveals global endodermal cell dynamics. Nat Commun. 2013;4(1):2207.","journal-title":"Nat Commun."},{"key":"5403_CR2","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12915-021-01037-w","volume":"19","author":"S Herbert","year":"2021","unstructured":"Herbert S, Valon L, Mancini L, Dray N, Caldarelli P, Gros J, Esposito E, Shorte SL, Bally-Cuif L, Aulner N, et al. LocalZProjector and DeProj: a toolbox for local 2D projection and accurate morphometrics of large 3D microscopy images. BMC Biol. 2021;19:1\u201313.","journal-title":"BMC Biol"},{"key":"5403_CR3","doi-asserted-by":"publisher","first-page":"1139","DOI":"10.1038\/nmeth.3648","volume":"12","author":"I Heemskerk","year":"2015","unstructured":"Heemskerk I, Streichan S. Tissue cartography: compressing bio-image data by dimensional reduction. 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Trainable Weka Segmentation: a machine learning tool for microscopy pixel classification. Bioinformatics. 2017;33(15):2424\u20136. https:\/\/doi.org\/10.1093\/bioinformatics\/btx180.","journal-title":"Bioinformatics"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-023-05403-z.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12859-023-05403-z\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-023-05403-z.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,7,12]],"date-time":"2023-07-12T10:02:12Z","timestamp":1689156132000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-023-05403-z"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,7,12]]},"references-count":8,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2023,12]]}},"alternative-id":["5403"],"URL":"https:\/\/doi.org\/10.1186\/s12859-023-05403-z","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,7,12]]},"assertion":[{"value":"31 March 2023","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"27 June 2023","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"12 July 2023","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"All procedures were done following the bioethical guidelines determined by the Ethics Commission of the Faculty of Medicine, Universidad de Chile.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"283"}}