{"version":1,"kind":"Article","sha256":"","slug":"19","location":"","dependencies":[],"doi":"10.54294/abscne","frontmatter":{"title":"ITK-based Registration of Large Images from Light Microscopy: A Biomedical Application","abstract":"Inactivation of the retinoblastoma gene in mouse embryos results\r\nin morphological changes in the placenta, which has been shown to\r\naffect fetal survivability. The construction of a 3D virtual\r\nplacenta aids in accurately quantifying structural changes using\r\nimage analysis. The placenta dataset consisted of 786 images\r\ntotaling 550 GB in size, which were registered into a volumetric\r\ndataset using ITK's registration framework. The registration\r\nprocess faces many challenges arising from the large image sizes,\r\ndamages during sectioning, staining gradients both within and\r\nacross sections, and background noise leading to local solutions.\r\nIn this work, we implement a rigorous ITK-based preprocessing\r\npipeline for removing noise and employ a novel 2-level\r\noptimization strategy for enhanced registration in ITK. We provide\r\n3D visualizations and numerical results to demonstrate our\r\nimprovements.","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":["Registration","Mutual Information","Optimization strategy","Light Microscopy"],"authors":[{"name":"Mosaliganti, Kishore","email":"kishoreraom@gmail.com","affiliations":["Harvard Medical School"],"corresponding":true},{"name":"Pan, Tony","affiliations":[]},{"name":"Machiraju, Raghu","email":"raghu.machiraju@gmail.com","affiliations":[]},{"name":"Huang, Kun","affiliations":[]},{"name":"Saltz, Joel","affiliations":[]}],"date_submitted":"2005-08-01T21:50:01Z","external_publication_id":19,"revision_cids":["bafkreif4ovdpkwwqzfav2ncb2fkgt3q73s2jack6kf4zb565lhl6i7yp2q"]},"mdast":{"type":"root"},"downloads":[{"url":"https://ipfs.desci.com/ipfs/bafkreia2yciid2e7x4vbzjqvl5cj6ontytawczw2hckdgbuoq66bpzhxlm","title":"root/insight-journal-metadata.json","filename":"insight-journal-metadata.json","extra":{"size_bytes":13551,"type":"file"}},{"url":"https://ipfs.desci.com/ipfs/bafkreifzpqpre7nlvq2lrnifyxdfycnmao3ggh36p3qx5etxdxa7cu3a3i","title":"root/reviews.md","filename":"reviews.md","extra":{"size_bytes":6709,"type":"file"}},{"url":"https://dweb.link/ipfs/bafybeihsysy66y3r6rzwd4izlnsv6whxdhrybiwz66qircpwsgzmsc3f3y","title":"root/article.pdf","filename":"article.pdf","extra":{"size_bytes":371236,"type":"file"}}],"references":{"cite":{"order":["ref1","ref2","ref3","ref4","ref5","ref6","ref7","ref8","ref9"]},"data":{"ref1":{"label":"ref1","enumerator":"1","url":"https://doi.org/10.1038/nature01262","html":"Consortium: Initial sequencing and comparative analysis of the mouse genome+Nature+520+2002+562+Mouse Genome Sequencing"},"ref2":{"label":"ref2","enumerator":"2","url":"https://doi.org/10.1038/nature01417","html":"Extra-embryonic function of Rb is essential for embryonic development and viability+Nature+942+2003+947+Wu+A. de Bruin+H.I. 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