{"version":1,"kind":"Article","sha256":"","slug":"14","location":"","dependencies":[],"doi":"10.54294/9nkczd","frontmatter":{"title":"Automated high-throughput registration for localizing 3D mouse brain gene expression using ITK","abstract":"The Allen Brain Atlas (ABA) project aims to create a\r\ncellular-resolution, genome-wide map of gene expression in the adult\r\nmouse brain. The resulting in situ hybridization (ISH) image data\r\nwill be available free-of-charge to the public. Additionally, we are\r\ndeveloping an informatics pipeline to support searching of the data by\r\nanatomic region and expression level and/or pattern. This paper\r\ndescribes a robust, high-throughput registration scheme to\r\nautomatically annotate hierarchical brain structures in the ISH\r\nimagery.","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":["High-throughput Processing","Mouse Gene Expression","Image Registration"],"authors":[{"name":"Ng, Lydia","email":"lydian@alleninstitute.org","affiliations":["Allen Institute for Brain Science"],"corresponding":true},{"name":"Hawrylycz, Michael","affiliations":[]},{"name":"Haynor, David","email":"haynor@u.washington.edu","affiliations":[]}],"date_submitted":"2005-07-29T20:52:39Z","external_publication_id":14,"revision_cids":["bafkreihopprecljmfpbuzvisf3iru6tih5myfhj42zftsjsdatphreoopy"]},"mdast":{"type":"root"},"downloads":[{"url":"https://pub.desci.com/ipfs/bafkreidmhzzoueojov3yxbor2bzmv6kvdxoy635crjmvtzpmvt7rwknkvi","title":"root/code/WorkshopCode/CMakeLists.txt","filename":"CMakeLists.txt","extra":{"size_bytes":610,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreihfp75bjsithnpysedevkfd6wlfoamszwc6hin6veeobqltpdgx6u","title":"root/code/WorkshopCode/DeformableRegistration6-mod.cxx","filename":"DeformableRegistration6-mod.cxx","extra":{"size_bytes":17119,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreieddfbp3tf76l6zguorv3xcxwfj76j6oh2wacdusimuemmoconagq","title":"root/code/WorkshopCode/ImageRegistration3-mod.cxx","filename":"ImageRegistration3-mod.cxx","extra":{"size_bytes":10472,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreiaxsx2uc6ohan5ecyjlcx6kwcfqzs7tp6b7zy354os7au66bppo64","title":"root/code/WorkshopCode/ReadMe.txt","filename":"ReadMe.txt","extra":{"size_bytes":1704,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreian5bplp7fgga5i3jdj76hzn33mkgpstsxqoaalx63tdkgxl7j6ti","title":"root/code/WorkshopCode/itkCombinedImageToImageMetricAdaptor.h","filename":"itkCombinedImageToImageMetricAdaptor.h","extra":{"size_bytes":4708,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreihhh4yvcf3zf6xlggxyu4km6zofnu5cn7lfyci4ofia2tnr2xlza4","title":"root/code/WorkshopCode/itkCombinedImageToImageMetricAdaptor.txx","filename":"itkCombinedImageToImageMetricAdaptor.txx","extra":{"size_bytes":6227,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreicoqlunruel7uipzuw6mdp7sucf2yqyyutj7cw4xqxhtzgprcpns4","title":"root/code/WorkshopCode/itkMeanSquaresImageToImageMetric2.h","filename":"itkMeanSquaresImageToImageMetric2.h","extra":{"size_bytes":5856,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreihgtxlutl7jp4ejfvayovsyjj7vqwooa5bj3zjqcm7ybvkjy7ewp4","title":"root/code/WorkshopCode/itkMeanSquaresImageToImageMetric2.txx","filename":"itkMeanSquaresImageToImageMetric2.txx","extra":{"size_bytes":9799,"type":"file"}},{"url":"https://ipfs.desci.com/ipfs/bafkreicss5tl7fam3cj2nvyxr2b3463dux5tojpfvfermjunhl3fnic6gi","title":"root/insight-journal-metadata.json","filename":"insight-journal-metadata.json","extra":{"size_bytes":6225,"type":"file"}},{"url":"https://dweb.link/ipfs/bafkreibnlbgqz6sjbf4tftb5jx7mbsoeqbbvmxjqadc2yu7lf44w5dhvmi","title":"root/article.pdf","filename":"article.pdf","extra":{"size_bytes":267731,"type":"file"}}],"references":{"cite":{"order":["ref1","ref2","ref3","ref4","ref5","ref6","ref7","ref8"]},"data":{"ref1":{"label":"ref1","enumerator":"1","url":"https://doi.org/10.1038/nature05453","html":"High throughput gene expression mapping in the mouse brain+In: The Biology of Genome+2005+S. 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