{"version":1,"kind":"Article","sha256":"","slug":"116","location":"","dependencies":[],"doi":"10.54294/2mw8nl","frontmatter":{"title":"I-DO: A Deformable Organisms framework for ITK","abstract":"Medical image analysis is an important problem relating to\r\nthe study of various diseases. Since their inception to MICCAI in\r\n2001, ''deformable organisms'' have emerged as a fruitful\r\nmethodology with examples ranging from 2D corpus callosum\r\nsegmentation to 3D vasculature and spinal cord segmentation.\r\nEssentially we have developed an artificial life framework that\r\ncomplements classical deformable models (snakes and deformable\r\nmeshes) with high-level, anatomically-driven control mechanisms.\r\nThis paper describes the integration of deformable organisms\r\ninto the Insight Toolkit (ITK) \\url{www.itk.org}. Our code attempts\r\nto bridge the ITK framework and coding style with deformable organism\r\ndesign methodologies. In the interest of open science, as the\r\nframework develops it will serve as a basis for the community to\r\ndevelop new deformable organisms as well as experiment with those\r\nrecently published by our group.","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":["segmentation","deformable organisms","ITK","deformable models","medical image analysis"],"authors":[{"name":"McIntosh, Chris","email":"cmcintos@cs.sfu.ca","affiliations":["Medical Image Analysis Lab, Simon Fraser University"],"corresponding":true},{"name":"Hamarneh, Ghassan","email":"hamarneh@cs.sfu.ca","affiliations":[]}],"date_submitted":"2006-07-14T01:29:45Z","external_publication_id":116,"revision_cids":["bafkreiakl4p6of6beyhqzm5hceul3dwboi4ffvslflbjec4k2cethy56xu"]},"mdast":{"type":"root"},"downloads":[{"url":"https://ipfs.desci.com/ipfs/bafkreidrmflctwscdqezdubxzx223e5f5gtprepdlaqxx3pi3prpacxvza","title":"root/insight-journal-metadata.json","filename":"insight-journal-metadata.json","extra":{"size_bytes":5456,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreihpi5rt4adfjpqksoeuilsnnnd2yd3alsmr4hz7gkbcwytiqbgtre","title":"root/code/CMakeLists.txt","filename":"CMakeLists.txt","extra":{"size_bytes":3172,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreicyta3inw6ilixlzxperu5lo2c6act3nlgcar7o55244cq5n4e6li","title":"root/code/CMakeTemplate.txt","filename":"CMakeTemplate.txt","extra":{"size_bytes":1918,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreigi7yaxzxym5hdiptzp2xhxbjrfeoh5cmirtid7cike6hiycd22qy","title":"root/code/IJMacros.txt","filename":"IJMacros.txt","extra":{"size_bytes":3205,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreibkmvwafbdnl5eu3wo3mbsngdakpjngxd44bxtbpeovnvaktafvcu","title":"root/code/ImageCompare.cxx","filename":"ImageCompare.cxx","extra":{"size_bytes":8164,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreia2xs2rejnmpujqp2la5ehpqow5i56dqunulp5fmllvyjjqw4n6zy","title":"root/code/source/sensory/Sense_AvgIntensity.cxx","filename":"Sense_AvgIntensity.cxx","extra":{"size_bytes":2132,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreicdykkynr7muaz6shueffffuoxbomgteff2vyeeu5kwm4hm2fibya","title":"root/code/source/sensory/Sense_AvgIntensity.h","filename":"Sense_AvgIntensity.h","extra":{"size_bytes":3249,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreiddyo5wadlxprusietpplmapbxkixxzz26jjrd63iv3nehkxhozoe","title":"root/code/source/sensory/Sense_Gradient.cxx","filename":"Sense_Gradient.cxx","extra":{"size_bytes":2056,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreibci57lf3bplnhj7rro6f2o3l5xapwai6nyt4c6xp3g7fguffvwry","title":"root/code/source/sensory/Sense_Gradient.h","filename":"Sense_Gradient.h","extra":{"size_bytes":3889,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreibjixujioteoqqkdzs4svlsuizymxm6xqlci73frj6ehbpwt3gg34","title":"root/code/source/sensory/abc/Sensor.cxx","filename":"Sensor.cxx","extra":{"size_bytes":151,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreidcgukpwzqekvx4zpmbmwmuiph2hayuxmso62zmgmhwacq5omxoxi","title":"root/code/source/sensory/abc/Sensor.h","filename":"Sensor.h","extra":{"size_bytes":2656,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreihhaudsryaua55yzush2jvyl3gmdsramc2jcqdd7ku6f5gq5jflqm","title":"root/code/source/physical/Def_Translation.cxx","filename":"Def_Translation.cxx","extra":{"size_bytes":1683,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreigr5zkhyk6ufkyfdp5vtrgrperfjg4ibt5kaw5m6mq2t6vuk4ykmi","title":"root/code/source/physical/Def_Translation.h","filename":"Def_Translation.h","extra":{"size_bytes":2573,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreic7m3xz52chqb77w75wsi4awz4acmft2juqnfgroc7f45yyo6lcvq","title":"root/code/source/physical/Def_UniformScale.cxx","filename":"Def_UniformScale.cxx","extra":{"size_bytes":1446,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreib3ktdch4624lulgwx5q3xrfzq2okofnkx2iwsh6nloze4pqe5u7a","title":"root/code/source/physical/Def_UniformScale.h","filename":"Def_UniformScale.h","extra":{"size_bytes":2514,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreiaplcvvgnrjkadtnlm5psmf77j2tn4oocerwgbvcaz7ytkcywg2py","title":"root/code/source/physical/Def_UniformScaleLevelSet.cxx","filename":"Def_UniformScaleLevelSet.cxx","extra":{"size_bytes":1665,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreidxbzwwtjcsffembcvhy5dcoztda3opisep7wq2nsjgd5sbfewoli","title":"root/code/source/physical/Def_UniformScaleLevelSet.h","filename":"Def_UniformScaleLevelSet.h","extra":{"size_bytes":2923,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreialfhwmpv3nomr47kqhqfs4yxlapcu7pl55djw7osd5rpaxj3vlji","title":"root/code/source/physical/Phys_Euler.cxx","filename":"Phys_Euler.cxx","extra":{"size_bytes":15925,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreihyd2qnb4n63n54wxaolfwmivmmabfaukcbzr5vnem764izcjctv4","title":"root/code/source/physical/Phys_Euler.h","filename":"Phys_Euler.h","extra":{"size_bytes":7314,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreiht7iza4z3pk5wzfnsqwdnyhghbvnhihm6j3zivyuqh7a5iszat3u","title":"root/code/source/physical/Phys_LevelSet.cxx","filename":"Phys_LevelSet.cxx","extra":{"size_bytes":13655,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreiekmixqpbckzoj642ly6p2r3p7gmposptziutuoft2p7hmel7drpe","title":"root/code/source/physical/Phys_LevelSet.h","filename":"Phys_LevelSet.h","extra":{"size_bytes":5166,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreihjb5qgr4ld3nbzhm5subjcb3iosbhg655yeujwedymy3xiybimfy","title":"root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ometric.cxx","filename":"Geometric.cxx","extra":{"size_bytes":112,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreiapykj5k32jw5kxmoccm6rpqqyqvs2kulmb2dhck34allnn52sgai","title":"root/code/source/geometrical/abc/Geometric.h","filename":"Geometric.h","extra":{"size_bytes":9397,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreiceet4hqz2l4a54qoxjqjbivkc7gvqbdjszbpetvcsh66gfx6yvfy","title":"root/code/source/cognitive/Ctrl_ScheduleDriven.cxx","filename":"Ctrl_ScheduleDriven.cxx","extra":{"size_bytes":1318,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreick4a7qqu4t67pxziptleoarevirwpka3ngdsatx3ob3rumdzlkwq","title":"root/code/source/cognitive/Ctrl_ScheduleDriven.h","filename":"Ctrl_ScheduleDriven.h","extra":{"size_bytes":1681,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreigurbxjevcdeeg4z4v55ubkh5qnml5rokktrjieuglwf4rrgoe5ve","title":"root/code/source/cognitive/Ctrl_SensoryDriven.cxx","filename":"Ctrl_SensoryDriven.cxx","extra":{"size_bytes":250,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreigkuy7z4hlodw53izlp4bg3jlmbrlhxp5rhyoystasabug3aaceha","title":"root/code/source/cognitive/Ctrl_SensoryDriven.h","filename":"Ctrl_SensoryDriven.h","extra":{"size_bytes":480,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreid5cwfqedwklw2j52l3bx3wsm547xzeyektuqmiota2t6o73rgbxm","title":"root/code/source/cognitive/abc/ControlCenter.cxx","filename":"ControlCenter.cxx","extra":{"size_bytes":1019,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreif2hvmqclpu4l5txjmtxwh465hctcwofadcu4ioevm3tp5qtwm7yi","title":"root/code/source/cognitive/abc/ControlCenter.h","filename":"ControlCenter.h","extra":{"size_bytes":4856,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreieeukvhyk5qz52awqw6bxhjktxyb56iz7edm5hs5utxspcoocoelq","title":"root/code/source/behavioral/Beh_SearchForObject.cxx","filename":"Beh_SearchForObject.cxx","extra":{"size_bytes":4330,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreid336x3hzt7qeibwqsv4jm45ukexku7c2yesslhspcxgmlz52ap6i","title":"root/code/source/behavioral/Beh_SearchForObject.h","filename":"Beh_SearchForObject.h","extra":{"size_bytes":3888,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreihklcmjtpbs5k33bxbm3t2rfev5wjcbu2f3hgo6ohlx2xzhupkbfq","title":"root/code/source/behavioral/Beh_TranslateAll.cxx","filename":"Beh_TranslateAll.cxx","extra":{"size_bytes":1974,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreieyq2ndzozlq3hnshl26fwt3xma7mrpfpriblwdbe4aptuxn73bqe","title":"root/code/source/behavioral/Beh_TranslateAll.h","filename":"Beh_TranslateAll.h","extra":{"size_bytes":2777,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreibrcdjsiebrgkple5pr77xuorl5l4ixx5vclfiktenwv4maquoxjy","title":"root/code/source/behavioral/Beh_UniformScale.cxx","filename":"Beh_UniformScale.cxx","extra":{"size_bytes":1583,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreibj256roa4qeyzvlerj3tyhzb43bzfng5pqi2sq6bdtw352igcssm","title":"root/code/source/behavioral/Beh_UniformScale.h","filename":"Beh_UniformScale.h","extra":{"size_bytes":2789,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreigibilkoxlxo6bmsfbuvtnq3y757qitmm2jtgy4c6woxo6n7oklue","title":"root/code/source/behavioral/abc/Behavior.cxx","filename":"Behavior.cxx","extra":{"size_bytes":219,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreienwp23h3qvfqiec4bk7xm35pohlec4jfihp7qsm45b5q62sjjjra","title":"root/code/source/behavioral/abc/Behavior.h","filename":"Behavior.h","extra":{"size_bytes":5547,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreihjo4kktxrf3xr7ks3bwi3khweepv7f6cnrru5i2t2n6i63m5szy4","title":"root/code/examples/CMakeLists.txt","filename":"CMakeLists.txt","extra":{"size_bytes":158,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreie7tx33tbqchdvsg4xdii4hj4lyup3ksep23amtlrayyq22bqwha4","title":"root/code/examples/basic/CMakeLists.txt","filename":"CMakeLists.txt","extra":{"size_bytes":1430,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreibhok42e2sagld5kdut5oixyp3tnn7fvlcxgdhu4esqxfycn5by3y","title":"root/code/examples/basic/defOrg.cxx","filename":"defOrg.cxx","extra":{"size_bytes":4650,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreiau6ite44mortqwioc57y7aj7yajcahbp663z7y62kdcqlj6xxsxm","title":"root/code/examples/advanced/CMakeLists.txt","filename":"CMakeLists.txt","extra":{"size_bytes":1497,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreieapjmwadllaognjpfob3a3mxrh5qtxxkbtw2lbifb7eu4rsbykom","title":"root/code/examples/advanced/defOrg.cxx","filename":"defOrg.cxx","extra":{"size_bytes":3464,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreigjq33odqxwh3rfehhos6gp5cy4fezjcahlmytsjqcotosdifdqgu","title":"root/code/examples/DefOrgViewerWithKW/Source/BYUToMeta.cxx","filename":"BYUToMeta.cxx","extra":{"size_bytes":3038,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreiegtf2guhzq77s3jhhqkhp2axie6vmyedjna5slk6wlzltzex2fii","title":"root/code/examples/DefOrgViewerWithKW/Source/BYUToMeta.h","filename":"BYUToM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