{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,5]],"date-time":"2024-08-05T05:19:15Z","timestamp":1722835155691},"reference-count":23,"publisher":"Walter de Gruyter GmbH","issue":"1","license":[{"start":{"date-parts":[[2020,1,1]],"date-time":"2020-01-01T00:00:00Z","timestamp":1577836800000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Tissue clearing methods have boosted the microscopic observations of thick samples such as whole-mount mouse or zebrafish. Even with the best tissue clearing methods, specimens are not completely transparent and light attenuation increases with depth, reducing signal output and signal-to-noise ratio. In addition, since tissue clearing and microscopic acquisition techniques have become faster, automated image analysis is now an issue. In this context, mounting specimens at large scale often leads to imperfectly aligned or oriented samples, which makes relying on predefined, sample-independent parameters to correct signal attenuation impossible.<\/jats:p>\n               <jats:p>Here, we propose a sample-dependent method for contrast correction. It relies on segmenting the sample, and estimating sample depth isosurfaces that serve as reference for the correction. We segment the brain white matter of zebrafish larvae. We show that this correction allows a better stitching of opposite sides of each larva, in order to image the entire larva with a high signal-to-noise ratio throughout. We also show that our proposed contrast correction method makes it possible to better recognize the deep structures of the brain by comparing manual vs. automated segmentations. This is expected to improve image observations and analyses in high-content methods where signal loss in the samples is significant.<\/jats:p>","DOI":"10.1515\/mathm-2020-0100","type":"journal-article","created":{"date-parts":[[2020,7,29]],"date-time":"2020-07-29T13:53:44Z","timestamp":1596030824000},"page":"31-45","source":"Crossref","is-referenced-by-count":1,"title":["Automated segmentation of thick confocal microscopy 3D images for the measurement of white matter volumes in zebrafish brains"],"prefix":"10.1515","volume":"4","author":[{"given":"Sylvain","family":"Lempereur","sequence":"first","affiliation":[{"name":"LIGM, Univ Gustave Eiffel , CNRS, ESIEE Paris, F-77454 Marne-la-Vall\u00e9e , France ,; Tefor Paris-Saclay, UMS2010, CNRS\/INRA, Universit\u00e9 Paris-Saclay , Gif sur Yvette , France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Arnim","family":"Jenett","sequence":"additional","affiliation":[{"name":"Tefor Paris-Saclay, UMS2010, CNRS\/INRA, Universit\u00e9 Paris-Saclay , Gif sur Yvette , France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Elodie","family":"Machado","sequence":"additional","affiliation":[{"name":"Tefor Paris-Saclay, UMS2010, CNRS\/INRA, Universit\u00e9 Paris-Saclay , Gif sur Yvette , France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ignacio","family":"Arganda-Carreras","sequence":"additional","affiliation":[{"name":"Ikerbasque, Basque Foundation for Science, Bilbao, Spain, Computer Science and Artificial Intelligence Department , University of the Basque Country, San Sebastian, Spai, Donostia International Physics Center , San Sebastian , Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Matthieu","family":"Simion","sequence":"additional","affiliation":[{"name":"Tefor Paris-Saclay, UMS2010, CNRS\/INRA, Universit\u00e9 Paris-Saclay , Gif sur Yvette , France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pierre","family":"Affaticati","sequence":"additional","affiliation":[{"name":"Tefor Paris-Saclay, UMS2010, CNRS\/INRA, Universit\u00e9 Paris-Saclay , Gif sur Yvette , France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jean-St\u00e9phane","family":"Joly","sequence":"additional","affiliation":[{"name":"Tefor Paris-Saclay, UMS2010, CNRS\/INRA, Universit\u00e9 Paris-Saclay , Gif sur Yvette , France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hugues","family":"Talbot","sequence":"additional","affiliation":[{"name":"LIGM, Univ Gustave Eiffel , CNRS, ESIEE Paris, F-77454 Marne-la-Vall\u00e9e, France, Universit\u00e9 Paris-Saclay, CentraleSup\u00e9lec, Inria, 91190 , Gif-sur-Yvette , France"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"374","published-online":{"date-parts":[[2020,7,27]]},"reference":[{"key":"2022042712261287882_j_mathm-2020-0100_ref_001_w2aab3b7b4b1b6b1ab1ab1Aa","doi-asserted-by":"crossref","unstructured":"[1] Pierre Affaticati, Matthieu Simion, Elodie De Job, Laurie Rivi\u00e8re, Jean-Michel Hermel, Elodie Machado, Jean-St\u00e9phane Joly, and Arnim Jenett. zPACT: Tissue Clearing and Immunohistochemistry on Juvenile Zebrafish Brain. 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