{"id":1950,"date":"2018-12-15T11:48:49","date_gmt":"2018-12-15T16:48:49","guid":{"rendered":"https:\/\/my.dev.vanderbilt.edu\/masi\/?p=1950"},"modified":"2018-12-19T16:56:39","modified_gmt":"2018-12-19T21:56:39","slug":"1950","status":"publish","type":"post","link":"https:\/\/my.dev.vanderbilt.edu\/masi\/2018\/12\/1950\/","title":{"rendered":"A Web-based Combined MRI-Histology Digital Atlas of the Squirrel Monkey Brain."},"content":{"rendered":"

Kurt G. Schilling, Yurui Gao, Vaibhav Janve, Matthew Christian, Iwona Stepniewska, Bennett A. Landman, Adam W. Anderson. \u201cA Web-based Combined MRI-Histology Digital Atlas of the Squirrel Monkey Brain.\u201d Neuroinformatics (2018) 1-15. doi:10.1007\/s12021-018-9391-z.<\/p>\n

Full text: https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/?term=A+Web-based+Combined+MRI-Histology+Digital+Atlas<\/strong><\/p>\n

Abstract<\/h2>\n
\u00a0The squirrel monkey (Saimiri sciureus) is a commonly-used surrogate for humans in biomedical research. In the neuroimaging community, MRI and histological atlases serve as valuable resources for anatomical, physiological, and functional studies of the brain; however, no digital<\/span> MRI\/histology atlas<\/span> is currently available for the squirrel monkey. This paper describes the construction of a web-based<\/span> multi-modal atlas<\/span> of the squirrel monkey brain. The MRI-derived information includes anatomical MRI contrast (i.e., T2-weighted and proton-density-weighted) and diffusion MRI metrics (i.e., fractional anisotropy and mean diffusivity) from data acquired both in vivo and ex vivo on a 9.4 Tesla scanner. The histological images include Nissl and myelin stains, co-registered to the corresponding MRI, allowing identification of cyto- and myelo-architecture. In addition, a bidirectional neuronal tracer, biotinylated dextran amine (BDA) was injected into the primary motor cortex, enabling highly specific identification of regions connected to the injection location. The atlas<\/span>integrates the results of common image analysis methods including diffusion tensor imaging glyphs, labels of 57 white-matter tracts identified using DTI-tractography, and 18 cortical regions of interest identified from Nissl-revealed cyto-architecture. All data are presented in a common space, and all image types are accessible through a web-based<\/span> atlas<\/span> viewer, which allows visualization and interaction of user-selectable contrasts and varying resolutions. By providing an easy to use reference system of anatomical information, our web-accessible multi-contrast atlas<\/span> forms a rich and convenient resource for comparisons of brain findings across subjects or modalities. The atlas<\/span> is called the Combined<\/span> Histology-MRI Integrated Atlas<\/span> of the Squirrel Monkey (CHIASM). All images are accessible through our web-based<\/span> viewer ( https:\/\/chiasm.vuse.vanderbilt.edu \/), and data are available for download at ( https:\/\/www.nitrc.org\/projects\/smatlas\/ ).<\/div>\n

Keywords:<\/b><\/p>\n

Histology; MRI; Squirrel monkey; User interactive; Web-based<\/span> atlas<\/span><\/p>\n

\"Atlas
Atlas interface and functionality. The toolbars, menus, and display associated with MRI (a) and histology (b) modalities are shown<\/figcaption><\/figure>\n","protected":false},"excerpt":{"rendered":"

Kurt G. Schilling, Yurui Gao, Vaibhav Janve, Matthew Christian, Iwona Stepniewska, Bennett A. Landman, Adam W. Anderson. \u201cA Web-based Combined MRI-Histology Digital Atlas of the Squirrel Monkey Brain.\u201d Neuroinformatics (2018) 1-15. doi:10.1007\/s12021-018-9391-z. Full text: https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/?term=A+Web-based+Combined+MRI-Histology+Digital+Atlas Abstract \u00a0The squirrel monkey (Saimiri sciureus) is a commonly-used surrogate for humans in biomedical research. In the neuroimaging community, MRI…<\/p>\n","protected":false},"author":6324,"featured_media":1951,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[9,4,1,49],"tags":[],"class_list":["post-1950","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-diffusion-weighted-mri","category-neuroimaging","category-news","category-tractography"],"_links":{"self":[{"href":"https:\/\/my.dev.vanderbilt.edu\/masi\/wp-json\/wp\/v2\/posts\/1950","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/my.dev.vanderbilt.edu\/masi\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/my.dev.vanderbilt.edu\/masi\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/my.dev.vanderbilt.edu\/masi\/wp-json\/wp\/v2\/users\/6324"}],"replies":[{"embeddable":true,"href":"https:\/\/my.dev.vanderbilt.edu\/masi\/wp-json\/wp\/v2\/comments?post=1950"}],"version-history":[{"count":2,"href":"https:\/\/my.dev.vanderbilt.edu\/masi\/wp-json\/wp\/v2\/posts\/1950\/revisions"}],"predecessor-version":[{"id":1953,"href":"https:\/\/my.dev.vanderbilt.edu\/masi\/wp-json\/wp\/v2\/posts\/1950\/revisions\/1953"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/my.dev.vanderbilt.edu\/masi\/wp-json\/wp\/v2\/media\/1951"}],"wp:attachment":[{"href":"https:\/\/my.dev.vanderbilt.edu\/masi\/wp-json\/wp\/v2\/media?parent=1950"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/my.dev.vanderbilt.edu\/masi\/wp-json\/wp\/v2\/categories?post=1950"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/my.dev.vanderbilt.edu\/masi\/wp-json\/wp\/v2\/tags?post=1950"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}