{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:38:59Z","timestamp":1740184739402,"version":"3.37.3"},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"23","funder":[{"name":"the Agency for Innovation by Science and Technology in Flanders","award":["IWT_140775","IWT_150003"],"award-info":[{"award-number":["IWT_140775","IWT_150003"]}]},{"name":"the Flemish Institute for Scientific Research","award":["11ZF116N"],"award-info":[{"award-number":["11ZF116N"]}]},{"DOI":"10.13039\/501100007660","name":"the University of Antwerp","doi-asserted-by":"crossref","award":["UA_29267"],"award-info":[{"award-number":["UA_29267"]}],"id":[{"id":"10.13039\/501100007660","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,12,1]]},"abstract":"<jats:p>Summary: Deep tissue imaging is increasingly used for non-destructive interrogation of intact organs and small model organisms. An intuitive approach to increase the imaging depth by almost a factor of 2 is to record a sample from two sides and fuse both image stacks. However, imperfect three-dimensional alignment of both stacks presents a computational challenge. We have developed a FIJI plugin, called BiDiFuse, which merges bi-directionally recorded image stacks via 3D rigid transformations. The method is broadly applicable, considering it is compatible with all optical sectioning microscopes and it does not rely on fiducial markers for image registration.<\/jats:p>\n               <jats:p>Availability and Implementation: The method is freely available as a plugin for FIJI from https:\/\/github.com\/JanDetrez\/BiDiFuse\/.<\/jats:p>\n               <jats:p>Contact: \u00a0winnok.devos@uantwerpen.be<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw515","type":"journal-article","created":{"date-parts":[[2016,8,9]],"date-time":"2016-08-09T01:43:59Z","timestamp":1470707039000},"page":"3691-3693","source":"Crossref","is-referenced-by-count":2,"title":["BiDiFuse: a FIJI plugin for fusing bi-directionally recorded microscopic image volumes"],"prefix":"10.1093","volume":"32","author":[{"given":"Jan R.","family":"Detrez","sequence":"first","affiliation":[{"name":"1Laboratory of Cell Biology & Histology, Department of Veterinary Sciences, University of Antwerp, 2020 Antwerp, Belgium"}]},{"given":"Jean-Marie","family":"Vanderwinden","sequence":"additional","affiliation":[{"name":"2Light Microscopy Facility & Laboratory of Neurophysiology, Faculty of Medicine, Free University of Brussels, 1070 Anderlecht, Belgium"}]},{"given":"Micha\u00ebl","family":"Barbier","sequence":"additional","affiliation":[{"name":"1Laboratory of Cell Biology & Histology, Department of Veterinary Sciences, University of Antwerp, 2020 Antwerp, Belgium"},{"name":"3Department of Neuroscience, Janssen Research and Development, 2340 Beerse, Belgium"}]},{"given":"Marlies","family":"Verschuuren","sequence":"additional","affiliation":[{"name":"1Laboratory of Cell Biology & Histology, Department of Veterinary Sciences, University of Antwerp, 2020 Antwerp, Belgium"}]},{"given":"Rony","family":"Nuydens","sequence":"additional","affiliation":[{"name":"3Department of Neuroscience, Janssen Research and Development, 2340 Beerse, Belgium"}]},{"given":"Xavier","family":"Langlois","sequence":"additional","affiliation":[{"name":"3Department of Neuroscience, Janssen Research and Development, 2340 Beerse, Belgium"}]},{"given":"Jean-Pierre","family":"Timmermans","sequence":"additional","affiliation":[{"name":"1Laboratory of Cell Biology & Histology, Department of Veterinary Sciences, University of Antwerp, 2020 Antwerp, Belgium"}]},{"given":"Winnok H.","family":"De Vos","sequence":"additional","affiliation":[{"name":"1Laboratory of Cell Biology & Histology, Department of Veterinary Sciences, University of Antwerp, 2020 Antwerp, Belgium"},{"name":"4Department of Molecular Biotechnology, Ghent University, 9000 Ghent, Belgium"}]}],"member":"286","published-online":{"date-parts":[[2016,8,8]]},"reference":[{"key":"2023020114084574600_btw515-B1","doi-asserted-by":"crossref","first-page":"331","DOI":"10.1038\/nmeth1036","article-title":"Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain","volume":"4","author":"Dodt","year":"2007","journal-title":"Nat. Methods"},{"key":"2023020114084574600_btw515-B2","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1023\/B:VISI.0000029664.99615.94","article-title":"Distinctive image features from scale-invariant keypoints","volume":"60","author":"Lowe","year":"2004","journal-title":"Int. J. Comput. Vis"},{"key":"2023020114084574600_btw515-B3","doi-asserted-by":"crossref","first-page":"418","DOI":"10.1038\/nmeth0610-418","article-title":"Software for bead-based registration of selective plane illumination microscopy data","volume":"7","author":"Preibisch","year":"2010","journal-title":"Nat. Methods"},{"key":"2023020114084574600_btw515-B4","doi-asserted-by":"crossref","first-page":"246","DOI":"10.1016\/j.cell.2015.06.067","article-title":"Clarifying tissue clearing","volume":"162","author":"Richardson","year":"2015","journal-title":"Cell"},{"key":"2023020114084574600_btw515-B5","doi-asserted-by":"crossref","first-page":"676","DOI":"10.1038\/nmeth.2019","article-title":"FIJI: an open-source platform for biological-image analysis","volume":"9","author":"Schindelin","year":"2012","journal-title":"Nat. Methods"},{"key":"2023020114084574600_btw515-B6","doi-asserted-by":"crossref","first-page":"726","DOI":"10.1016\/j.cell.2014.03.042","article-title":"Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis","volume":"157","author":"Susaki","year":"2014","journal-title":"Cell"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/23\/3691\/49027272\/bioinformatics_32_23_3691.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/23\/3691\/49027272\/bioinformatics_32_23_3691.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T23:59:26Z","timestamp":1675295966000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/32\/23\/3691\/2525630"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,8,8]]},"references-count":6,"journal-issue":{"issue":"23","published-print":{"date-parts":[[2016,12,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btw515","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2016,12,1]]},"published":{"date-parts":[[2016,8,8]]}}}