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Manual segmentation has been widely used in the field of biological sciences for complex structures composed of several sub\u2010parts and can be a time\u2010consuming process. Many tools have been developed to automate the segmentation process, all with various limitations and advantages, however, multipart segmentation remains a largely manual process. The aim of this study was to develop an open\u2010access and user\u2010friendly tool for the automatic segmentation of calcified tissues, specifically focusing on craniofacial bones. Here we describe BounTI, a novel segmentation algorithm which preserves boundaries between separate segments through iterative thresholding. This study outlines the working principles behind this algorithm, investigates the effect of several input parameters on its outcome, and then tests its versatility on CT images of the craniofacial system from different species (e.g. a snake, a lizard, an amphibian, a mouse and a human skull) with various scan qualities. The case studies demonstrate that this algorithm can be effectively used to segment the craniofacial system of a range of species automatically. High\u2010resolution microCT images resulted in more accurate boundary\u2010preserved segmentation, nonetheless significantly lower\u2010quality clinical images could still be segmented using the proposed algorithm. Methods for manual intervention are included in this tool when the scan quality is insufficient to achieve the desired segmentation results. While the focus here was on the craniofacial system, BounTI can be used to automatically segment any hard tissue. The tool presented here is available as an Avizo\/Amira add\u2010on, a stand\u2010alone Windows executable, and a Python library. We believe this accessible and user\u2010friendly segmentation tool can benefit the wider anatomical community.<\/jats:p>","DOI":"10.1111\/joa.14063","type":"journal-article","created":{"date-parts":[[2024,5,18]],"date-time":"2024-05-18T05:19:18Z","timestamp":1716009558000},"page":"829-841","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":17,"title":["<scp>BounTI<\/scp> (boundary\u2010preserving threshold iteration): A user\u2010friendly tool for automatic hard tissue segmentation"],"prefix":"10.1111","volume":"245","author":[{"ORCID":"https:\/\/orcid.org\/0009-0008-5382-2493","authenticated-orcid":false,"given":"Marius","family":"Didziokas","sequence":"first","affiliation":[{"name":"Department of Mechanical Engineering University College London  London UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Erwin","family":"Pauws","sequence":"additional","affiliation":[{"name":"Developmental Biology and Cancer Research and Teaching Department, UCL Great Ormond Street Institute of Child Health University College London  London UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lars","family":"K\u00f6lby","sequence":"additional","affiliation":[{"name":"Department of Plastic Surgery, Sahlgrenska University Hospital University of Gothenburg  Gothenburg Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0649-1432","authenticated-orcid":false,"given":"Roman H.","family":"Khonsari","sequence":"additional","affiliation":[{"name":"Department of Maxillofacial Surgery and Plastic Surgery, Necker\u2014Enfants Malades Hospital, Assistance Publique\u2014H\u00f4pitaux de Paris; Faculty of Medicine Universit\u00e9 Paris Cit\u00e9  Paris France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9951-2975","authenticated-orcid":false,"given":"Mehran","family":"Moazen","sequence":"additional","affiliation":[{"name":"Department of Mechanical Engineering University College London  London UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2024,5,17]]},"reference":[{"key":"e_1_2_8_2_1","doi-asserted-by":"publisher","DOI":"10.3390\/app12126097"},{"key":"e_1_2_8_3_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467\u2010022\u201029637\u20102"},{"key":"e_1_2_8_4_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.tree.2014.04.004"},{"key":"e_1_2_8_5_1","doi-asserted-by":"publisher","DOI":"10.1098\/rspb.2017.0194"},{"key":"e_1_2_8_6_1","doi-asserted-by":"publisher","DOI":"10.1007\/s10237\u2010023\u201001799\u2010y"},{"key":"e_1_2_8_7_1","volume-title":"Fundamentals of craniofacial growth","author":"Dixon A.D.","year":"1997"},{"key":"e_1_2_8_8_1","doi-asserted-by":"publisher","DOI":"10.1111\/joa.13383"},{"key":"e_1_2_8_9_1","doi-asserted-by":"publisher","DOI":"10.1136\/bmj.324.7345.1077"},{"key":"e_1_2_8_10_1","doi-asserted-by":"publisher","DOI":"10.3722\/cadaps.2011.269\u2010288"},{"key":"e_1_2_8_11_1","doi-asserted-by":"publisher","DOI":"10.3390\/bioengineering10050604"},{"key":"e_1_2_8_12_1","doi-asserted-by":"publisher","DOI":"10.3389\/fninf.2019.00009"},{"key":"e_1_2_8_13_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.acra.2019.07.006"},{"key":"e_1_2_8_14_1","doi-asserted-by":"publisher","DOI":"10.1098\/rspb.2024.0654"},{"key":"e_1_2_8_15_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41598\u2010023\u201036646\u20108"},{"key":"e_1_2_8_16_1","doi-asserted-by":"publisher","DOI":"10.1148\/rg.2015140232"},{"key":"e_1_2_8_17_1","doi-asserted-by":"publisher","DOI":"10.1002\/ar.25168"},{"key":"e_1_2_8_18_1","doi-asserted-by":"publisher","DOI":"10.1111\/joa.14004"},{"key":"e_1_2_8_19_1","doi-asserted-by":"publisher","DOI":"10.1097\/PRS.0000000000010530"},{"key":"e_1_2_8_20_1","doi-asserted-by":"publisher","DOI":"10.1115\/1.4028985"},{"key":"e_1_2_8_21_1","doi-asserted-by":"publisher","DOI":"10.1109\/TSMC.1979.4310076"},{"key":"e_1_2_8_22_1","doi-asserted-by":"publisher","DOI":"10.4103\/0256\u20104602.113498"},{"key":"e_1_2_8_23_1","doi-asserted-by":"publisher","DOI":"10.1002\/cyto.a.22806"},{"key":"e_1_2_8_24_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12915\u2010020\u20100753\u20102"},{"key":"e_1_2_8_25_1","doi-asserted-by":"publisher","DOI":"10.26717\/BJSTR.2020.24.004031"},{"key":"e_1_2_8_26_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00401\u2010013\u20101104\u2010y"},{"key":"e_1_2_8_27_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0031\u20103203(99)00055\u20102"},{"key":"e_1_2_8_28_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.wneu.2022.06.050"},{"key":"e_1_2_8_29_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.medengphy.2017.10.008"}],"container-title":["Journal of Anatomy"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/joa.14063","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,11,8]],"date-time":"2024-11-08T18:28:57Z","timestamp":1731090537000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1111\/joa.14063"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,5,17]]},"references-count":28,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2024,12]]}},"alternative-id":["10.1111\/joa.14063"],"URL":"https:\/\/doi.org\/10.1111\/joa.14063","archive":["Portico"],"relation":{},"ISSN":["0021-8782","1469-7580"],"issn-type":[{"value":"0021-8782","type":"print"},{"value":"1469-7580","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,5,17]]},"assertion":[{"value":"2023-11-13","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2024-05-02","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2024-05-17","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}