{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,8]],"date-time":"2026-01-08T08:14:59Z","timestamp":1767860099586,"version":"3.49.0"},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"19","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: TiQuant is a modular software tool for efficient quantification of biological tissues based on volume data obtained by biomedical image modalities. It includes a number of versatile image and volume processing chains tailored to the analysis of different tissue types which have been experimentally verified. TiQuant implements a novel method for the reconstruction of three-dimensional surfaces of biological systems, data that often cannot be obtained experimentally but which is of utmost importance for tissue modelling in systems biology.<\/jats:p>\n               <jats:p>Availability and implementation: TiQuant is freely available for non-commercial use at msysbio.com\/tiquant. Windows, OSX and Linux are supported.<\/jats:p>\n               <jats:p>Contact: \u00a0hoehme@uni-leipzig.de<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv346","type":"journal-article","created":{"date-parts":[[2015,6,4]],"date-time":"2015-06-04T10:15:43Z","timestamp":1433412943000},"page":"3234-3236","source":"Crossref","is-referenced-by-count":24,"title":["TiQuant: software for tissue analysis, quantification and surface reconstruction"],"prefix":"10.1093","volume":"31","author":[{"given":"Adrian","family":"Friebel","sequence":"first","affiliation":[{"name":"1 Interdisciplinary Centre for Bioinformatics (IZBI), University of Leipzig, Germany,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Johannes","family":"Neitsch","sequence":"additional","affiliation":[{"name":"1 Interdisciplinary Centre for Bioinformatics (IZBI), University of Leipzig, Germany,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tim","family":"Johann","sequence":"additional","affiliation":[{"name":"1 Interdisciplinary Centre for Bioinformatics (IZBI), University of Leipzig, Germany,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Seddik","family":"Hammad","sequence":"additional","affiliation":[{"name":"2 Leibniz Research Centre for Working Environment and Human Factors (IfADo), Dortmund, Germany,"},{"name":"3 Department of Forensic Medicine and Veterinary Toxicology, Faculty of Veterinary Medicine, South Valley University, Qena, Egypt and"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jan G.","family":"Hengstler","sequence":"additional","affiliation":[{"name":"2 Leibniz Research Centre for Working Environment and Human Factors (IfADo), Dortmund, Germany,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dirk","family":"Drasdo","sequence":"additional","affiliation":[{"name":"1 Interdisciplinary Centre for Bioinformatics (IZBI), University of Leipzig, Germany,"},{"name":"4 Institut National de Recherche en Informatique et en Automatique (INRIA) Unit Rocquencourt, Le Chesnay Cedex, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stefan","family":"Hoehme","sequence":"additional","affiliation":[{"name":"1 Interdisciplinary Centre for Bioinformatics (IZBI), University of Leipzig, Germany,"},{"name":"4 Institut National de Recherche en Informatique et en Automatique (INRIA) Unit Rocquencourt, Le Chesnay Cedex, France"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2015,6,3]]},"reference":[{"key":"2023020202235714400_btv346-B1","doi-asserted-by":"crossref","DOI":"10.54294\/lf8u75","article-title":"The watershed transform in ITK discussion and new developments","author":"Beare","year":"2006","journal-title":"The Insight J."},{"key":"2023020202235714400_btv346-B2","doi-asserted-by":"crossref","first-page":"1161","DOI":"10.1007\/s00204-014-1243-5","article-title":"Protocols for staining of bile canalicular and sinusoidal networks of human, mouse and pig livers, three-dimensional reconstruction and quantification of tissue microarchitecture by image processing and analysis","volume":"88","author":"Hammad","year":"2014","journal-title":"Arch Toxicol."},{"key":"2023020202235714400_btv346-B3","doi-asserted-by":"crossref","first-page":"2641","DOI":"10.1093\/bioinformatics\/btq437","article-title":"A cell-based simulation software for multicellular systems","volume":"26","author":"Hoehme","year":"2010","journal-title":"Bioinformatics"},{"key":"2023020202235714400_btv346-B4","doi-asserted-by":"crossref","first-page":"10371","DOI":"10.1073\/pnas.0909374107","article-title":"Prediction and validation of cell alignment along microvessels as order principle to restore tissue architecture in liver regeneration","volume":"107","author":"Hoehme","year":"2010","journal-title":"Proc. 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