{ "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.", "authors": [ { "author_fullname": "Ng, Lydia", "author_place": 1, "persona_email": "lydian@alleninstitute.org", "persona_firstname": "Lydia", "persona_id": 64, "persona_lastname": "Ng" }, { "author_fullname": "Hawrylycz, Michael", "author_place": 2, "persona_id": null }, { "author_fullname": "Haynor, David", "author_place": 3, "persona_email": "haynor@u.washington.edu", "persona_firstname": "David", "persona_id": 405, "persona_lastname": "Haynor" } ], "categories": [], "comments": [], "date_submitted": "2005-07-29T20:52:39Z", "journals": [ { "journal_id": 3, "journal_name": "The Insight Journal" } ], "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", "publication_id": 14, "reviews": [], "revisions": [ { "article": "bafkreibnlbgqz6sjbf4tftb5jx7mbsoeqbbvmxjqadc2yu7lf44w5dhvmi", "citation_list": [ { "doi": "10.1038/nature05453", "key": "ref1", "score": 132.7137, "unstructured": "High throughput gene expression mapping in the mouse brain+In: The Biology of Genome+2005+S. Sunkin+A. Boe+K. Brockway+L. Chen+M. Chin+J. Chong+C. Dang+N. Dee+A. Desaki+T. Desta+H. Dong+A. Ebbert+C. Frensley+K. Halverson+M. Hart+M. Hawrylycz+E. Hill+M. Ishihara+Johnson+R. Kawal+J. Kidney+R. Knapik+L. Kuan+K. Larsen+E. Lein+L. Luong+J. Michaels+N. Mosqueda+M. Mortrud+L. Ng+G. Orta+S. Pathak+O. Pearson+R. Puchalski+T. Pak+Z. Riley+S. Rowland+J. Royall+N. Sarno+N. Shapovalova+A. Sherwood+B. Smith+K. Smith+S. Smith+A. Sodt+C. Slaughterbeck+N. Stewart+K.R. Stumpf+M. Sutram+C. Teemer+C. Thaller+C. Thompson+K. Wasell+R. Whitlock+P. Wohnoutka+B. Youngstrom+X. Yuan+A. Jones" }, { "doi": "10.1186/1471-2202-8-s2-p11", "key": "ref2", "score": 74.071594, "unstructured": "An automated informatics pipeline for computing 3d gene expression atlases+In: Society for Neuroscience, 35th Annual Meeting+2005+L. Chen+C. Dang+H.W. Dong+M. Hawrylycz+A. Jones+R. Kawal+L. Kuan+K. Larsen+C. Lein+E. Ng+L. Pathak+S. Teemer+C. Thompson+C. Sodt.+A. Sunkin+S. Wohnoutka+P.:+D.C." }, { "doi": "10.1007/978-3-540-30135-6_24", "key": "ref3", "score": 165.52989, "unstructured": "Landmark-driven, atlas-based segmentation of mouse brain tissue images containing gene expression data+In: Proc. 7th International Conference on Medical Image Computing+2004+192+199+I. Kakadiaris+M. Bello+S. Arunachalam+W. Kang+T. Ju+J. Warren+J. Carson+W. Chiu+C. Thaller+Eichele+Intervention Computer-Assisted" }, { "doi": "10.1109/csbw.2005.49", "key": "ref4", "score": 69.1224, "unstructured": "A geometric database for gene expression data+In: Proc. Eurographics Symposium on Geometry Processing+2003+166+176+T. Ju+J. Warren+G. Eichele+C. Thaller+W. Chiu+J.: Carson" }, { "doi": "10.1007/11784012_28", "key": "ref5", "score": 86.432106, "unstructured": "Using MRI to build a 3D reference atlas of the mouse brain from histology images+In: Proc. Intl. Soc. Magn. Res. Med+13+2005+2809+P. Yushkevich+B. Avants+Zhang+P. Burstein+L. Ng+M. Hawrylycz+Gee" }, { "doi": "10.1109/42.52980", "key": "ref6", "score": 97.93761, "unstructured": "Shape-based interpolation of multidimensional objects+IEEE Trans. on Medical Imaging+9+1990+32+42+S.P. Raya+J.K. Udupa" }, { "doi": "10.1109/tmi.2003.815867", "key": "ref7", "score": 126.48205, "unstructured": "Mutual-information-based registration of medical images: a survey+IEEE Trans. on Medical Imaging+22+2003+986+1004+J. Pluim+J. Maintz+M. Viergever" }, { "key": "ref8", "score": 28.25372, "unstructured": "The ITK Software Guide. Kitware, Inc. ISBN 1-930934-10-6+2003+L. Ibanez+W. Schroeder+L. Ng+J. Cates" } ], "dapp": null, "dataset": null, "doi": "10.54294/9nkczd", "handle": "1926/15", "source_code": "bafybeidscpgfn3gt2wfkvh6ztxgwftzkrtn6ad37646chl2nbiocqbju5q", "source_code_git_ref": null } ], "source_code_git_repo": null, "submitted_by_author": { "author_email": "lydian@alleninstitute.org", "author_firstname": "Lydia", "author_fullname": "Ng, Lydia", "author_id": 64, "author_institution": "Allen Institute for Brain Science", "author_lastname": "Ng" }, "tags": [ "High-throughput Processing", "Mouse Gene Expression", "Image Registration" ], "title": "Automated high-throughput registration for localizing 3D mouse brain gene expression using ITK" }