{"version":1,"kind":"Article","sha256":"","slug":"641","location":"","dependencies":[],"doi":"10.54294/2bq566","thumbnail":"https://pub.desci.com/ipfs/bafkreiddreviwqhrjxxcxpnxewborkxvbjdxpj3ylnqeq3pgjqlm5urszq","frontmatter":{"title":"Automatic Branch Decomposition for Tubular Structures","abstract":" Branches of tubular structures (vasculature, trachea, neuron, etc.) in medical images are critical for the topology of these structures. In many applications, It is very helpful to be able to decompose tubular structures and identify every individual branch. For example, quantification of geometric vascular features, registration of trachea movement due to respiration, tracing of neuron path. However, manual decomposition can be tedious, time-consuming, and subject to operator bias. In this paper, we propose a novel method to decompose tubular structures automatically and describe how to implement it in ITK framework. The input is a 2D/3D binary image that can be obtained from any segmentation techniques, as well as the junctions, which can be generated automatically from our previously contributed ITK class: itk::JunctionDetectionFilter. The output will be branches with their labels and their connection. There are only two parameters which need to be set by the user. We provide here the implementation as a ITK class: itk::BranchDecompositionFilter.\nPlease cite the following paper if you are interested in our work.\nG. Xiong, C. Chen, J. Chen, Y. Xie, and L. Xing, Tracking the Motion Trajectories of Junction Structures in 4D CT Images of the Lung, Vol. 57, No. 15, pp. 4905-4930, Physics in Medicine and Biology, 2012.","license":"You are licensing your work to Kitware Inc. under the\nCreative Commons Attribution License Version 3.0.\n\nKitware Inc. agrees to the following:\n\nKitware is free\n * to copy, distribute, display, and perform the work\n * to make derivative works\n * to make commercial use of the work\n\nUnder the following conditions:\n\\\"by Attribution\\\" - Kitware must attribute the work in the manner specified by the author or licensor.\n\n * For any reuse or distribution, they must make clear to others the license terms of this work.\n * Any of these conditions can be waived if they get permission from the copyright holder.\n\nYour fair use and other rights are in no way affected by the above.\n\nThis is a human-readable summary of the Legal Code (the full license) available at\nhttp://creativecommons.org/licenses/by/3.0/legalcode","keywords":["branch decomposition","vessel","domain decomposition","tubular structures","trachea","neuron","junction detection"],"authors":[{"name":"Xiong, Guanglei","email":"guangleixiong@gmail.com","affiliations":["Stanford University"],"corresponding":true},{"name":"Xing, Lei","affiliations":[]},{"name":"Taylor, Charles","affiliations":[]}],"date_submitted":"2009-05-05 01:34:35","external_publication_id":641,"revision_cids":["bafkreicb67vezfktusbxpxit5r7iftp6mdj23si7hpt6qwldybaxozntcm"],"github":"https://github.com/midas-journal/midas-journal-641.git","thumbnail":"https://pub.desci.com/ipfs/bafkreiddreviwqhrjxxcxpnxewborkxvbjdxpj3ylnqeq3pgjqlm5urszq"},"mdast":{"type":"root"},"downloads":[{"url":"https://pub.desci.com/ipfs/bafkreibmrgsom736m5a7dv2afzup32wk6j6voz4fjctop6dq2mivssae4i","title":"root/code/branchdecomposition/CMakeLists.txt","filename":"CMakeLists.txt","extra":{"size_bytes":2842,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreicyta3inw6ilixlzxperu5lo2c6act3nlgcar7o55244cq5n4e6li","title":"root/code/branchdecomposition/CMakeTemplate.txt","filename":"CMakeTemplate.txt","extra":{"size_bytes":1918,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreidsuvum4ihhamba3w5xnnhyu3rhrxzjtzkfggnmwokhpg7ktzqjxa","title":"root/code/branchdecomposition/IJMacros.txt","filename":"IJMacros.txt","extra":{"size_bytes":3465,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreibkmvwafbdnl5eu3wo3mbsngdakpjngxd44bxtbpeovnvaktafvcu","title":"root/code/branchdecomposition/ImageCompare.cxx","filename":"ImageCompare.cxx","extra":{"size_bytes":8164,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreia77tvcwytc2cdwp75x4rcv3ax6vmzfowolyir4bfthfqoy7ff3fm","title":"root/code/branchdecomposition/itkBranchDecompositionFilter.h","filename":"itkBranchDecompositionFilter.h","extra":{"size_bytes":4652,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreiegwd7r4n4s7xrnxx6tfsmwibcgama6jaw2qnpabmbcgpjvqa73nq","title":"root/code/branchdecomposition/itkBranchDecompositionFilter.txx","filename":"itkBranchDecompositionFilter.txx","extra":{"size_bytes":14174,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreicl7clzbp7deci4gkz22wrollcvvophkn3insjytnisfbb2bf7zze","title":"root/code/branchdecomposition/itkBranchDecompositionFilter2DTest.cxx","filename":"itkBranchDecompositionFilter2DTest.cxx","extra":{"size_bytes":4690,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreiexjsq3btmb5xyvnhhu3bfrtvddsa2rkqa4lmzppbmhkfrmgpmuue","title":"root/code/branchdecomposition/itkBranchDecompositionFilter3DTest.cxx","filename":"itkBranchDecompositionFilter3DTest.cxx","extra":{"size_bytes":4705,"type":"file"}},{"url":"https://ipfs.desci.com/ipfs/bafkreia7miifeabvt2e7rkleivfflqc5jey5sgvtj2deexla4dhcdia2w4","title":"root/insight-journal-metadata.json","filename":"insight-journal-metadata.json","extra":{"size_bytes":4469,"type":"file"}},{"url":"https://dweb.link/ipfs/bafkreibtjyzweause7xrfekyilf27lnpomto4c5qb576z5skrnlgerfqwa","title":"root/article.pdf","filename":"article.pdf","extra":{"size_bytes":388132,"type":"file"}}],"references":{"cite":{"order":["ref1","ref2","ref3"]},"data":{"ref1":{"label":"ref1","enumerator":"1","html":"Automatic Junction Detection for Tubular Structures+The Insight Journal+2009+G. Xiong+L. Xing+C. Taylor+Jan-Jun"},"ref2":{"label":"ref2","enumerator":"2","html":"The ITK Software Guide. Kitware, Inc. ISBN 1-930934-10-6+2003+L. Ibanez+W. Schroeder"},"ref3":{"label":"ref3","enumerator":"3","html":"1 Corresponding author: Guanglei Xiong: guangleixiong at gmail"}}}}