MBAT_v200 < MouseBIRN

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<h2><a name="ABOUT_THE_MOUSE_BIRN_ATLASING_TO"> </a> ABOUT THE MOUSE BIRN ATLASING TOOLKIT (<a class="twikiLink" href="/twiki/bin/view/MouseBIRN/MBAT">MBAT</a>) </h2>
<h4><a name="GENERAL_DESCRIPTION"> </a><a name="GENERAL_DESCRIPTION_"> </a> GENERAL DESCRIPTION: </h4>

The Mouse BIRN Atlasing Toolkit is designed to view multiple types of multiscale data, access and query databases associated with the Mouse BIRN, and process some of these data types.
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This is a collaborative effort by <a href="http://www.loni.ucla.edu/twiki/bin/view/MouseBIRN/MouseBIRNPartnerInstitutions" target="_top">the groups of the Mouse BIRN</a> to create an interoperable tool that offers an intuitive way to access the functionality offered by the individual efforts. The goal of the <a class="twikiLink" href="/twiki/bin/view/MouseBIRN/MBAT">MBAT</a> is to act as an intuitive, interoperable interface for viewing, accessing, processing, and analyzing multimodal data with emphasis on functionality across distributed locations and diverse databases.  This tool allows a user to view their data and offers the ability to interface with data offered by mouse BIRN. Future plans include the option to incorporate and compare a variety of different data types, regardless of user location or affiliation with the Mouse BIRN.
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Version: MBAT 2.0 beta, release November 2007
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Report Bugs at The <a href="https://cms.loni.ucla.edu/MBAT/forum.aspx?g=topics&amp;f=226" target="_top">BIRN help page</a>, or <a href="https://cms.loni.ucla.edu/MBAT/forum.aspx" target="_top">MBAT forum</a> of the <a href="http://cms.loni.ucla.edu/MBAT/index.aspx" target="_top">official LONI MBAT Website</a>

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    <tr><td valign="top"><img valign="top" src="/twiki/pub/MouseBIRN/MBAT/MBAT_home_1.jpg" alt="MBAT.jpg" /></td>
        <td rowspan="4"><img src="/twiki/pub/MouseBIRN/MBAT/mbat20b.jpg" alt="MBAT.jpg"  width="575" height="403"/></td></tr>
    <tr><td valign="top"><img valign="top" src="/twiki/pub/MouseBIRN/MBAT/MBAT_home_2.gif" alt="MBAT.jpg" /></td></tr>
    <tr><td valign="top"><img valign="top" src="/twiki/pub/MouseBIRN/MBAT/MBAT_home_3.jpg" alt="MBAT.jpg" /></td></tr>
    <tr><td valign="top"><img valign="top" src="/twiki/pub/MouseBIRN/MBAT/MBAT_home_4.jpg" alt="MBAT.jpg" /></td></tr>
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<h4><a name="FEATURES"> </a><a name="FEATURES_"> </a> FEATURES: </h4>

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<dt> <strong>DATA QUERIES</strong> </dt><dd> One of the main goals of the Mouse BIRN collaboration is to make querying and accessing multiple data types and sources within the context of a digital atlas easy and intuitive. To achieve these goals, there are two new query options available. 
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<dt> <strong>Concept-based Queries</strong> </dt><dd> The query interface allows the use to search data by date type, subject, and experiment related terms. A query may return multiple types of data most of which can be viewed within <a class="twikiLink" href="/twiki/bin/view/MouseBIRN/MBAT">MBAT</a>. For those that cannot, a link to an external website may be provided.
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<dt> <strong>Spatial-based Queries</strong> </dt><dd> Spatial-based queries allow the user to search data based on a region of interest in the atlas. This query system has been built suing functionality developed for UCSD's SmartAtlas. The system access 2D images that have been registered using tools developed by the UCSD group.

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<dt> <strong>EM/Cell Queries</strong> </dt><dd> High resolution cell fills and brain maps spatially linked to the <a class="twikiLink" href="/twiki/bin/view/MouseBIRN/MBAT">MBAT</a> atlases can be located, viewed, and downloaded. This query tool accesses the database at <a href="http://ccdb.ucsd.edu/CCDBWebSite/index.html" target="_top">CCDB</a>.
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<dt> <strong>Expression Queries</strong> </dt><dd> Expression queries allow the user to search for microarray gene expression data from different databases. This includes the <a href="http://www.genenetwork.org" target="_top">GeneNetwork database <a href="http://www.genenetwork.org</a>" target="_top">http://www.genenetwork.org]]</a> and the <a href="http://microarray.nbirn.net/index.html" target="_top">BIRN Microarray database <a href="http://microarray.nbirn.net/index.html</a>" target="_top">http://microarray.nbirn.net/index.html]]</a>. The return of the query is shown as color values corresponding to gene expression levels for some areas of the brain.

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<dt> <strong>ATLASES</strong> </dt><dd>  <a class="twikiLink" href="/twiki/bin/view/MouseBIRN/MBAT">MBAT</a> is distributed in two different versions, a standalone version and a full atlas version.The atlas version is packaged with an MR data file, a delineation (MDA2006), 3D surfaces that can be viewed with <a class="twikiLink" href="/twiki/bin/view/MouseBIRN/MBAT">MBAT</a> 3D Viewer and Surface Manager, and a structural hierarchy that can be viewed and navigated through using the <a href="http://www.loni.ucla.edu/twiki/bin/view/MouseBIRN/BrainGraph" target="_top">BrainGraph</a> tool.  Several additional atlas delinations are available for download at <a href="http://www.nbirn.net/bdr/bdr_current_data.shtm" target="_top">http://www.nbirn.net/bdr/bdr_current_data.shtm</a>. 

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<dt> <strong>DATA VOLUMES</strong> </dt><dd>  <a class="twikiLink" href="/twiki/bin/view/MouseBIRN/MBAT">MBAT</a> provides the user with the option of downloading several different data volumes for visualization purposes.  These data volumes were created by the Mouse BIRN group and are available in the Analyze image 7.5 format.  It also is possible to load other types of image volumes/datasets into the main <a class="twikiLink" href="/twiki/bin/view/MouseBIRN/MBAT">MBAT</a> viewer.  These datasets can be found on the BIRN download site <a href="http://www.nbirn.net/" target="_top">BIRN site</a> or here.
</dd>
<dt> <strong>BrainGraph</strong> </dt><dd> <a class="twikiLink" href="/twiki/bin/view/MouseBIRN/BrainGraph">BrainGraph</a> is a flexible, extensible, graph-based data model that integrates, organizes and directly accesses numerous types of data.  It allows simultaneous storage of multiple labeling schemes and study-specific graph traversal schemes. The <a class="twikiLink" href="/twiki/bin/view/MouseBIRN/BrainGraph">BrainGraph</a> editor has been integrated into the <a class="twikiLink" href="/twiki/bin/view/MouseBIRN/MBAT">MBAT</a> application.  <a class="twikiLink" href="/twiki/bin/view/MouseBIRN/BrainGraph">BrainGraph</a> adds colored label nodes that correspond to the label volume and label index.  This makes it easier for the user to identify and navigate the brain structures. Also, the new tree view option provides clearer and organized hierarchical information of structures to view the brain.

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<dt> <strong>Workspaces</strong> </dt><dd> <a class="twikiLink" href="/twiki/bin/view/MouseBIRN/MBAT">MBAT</a> offers different Workspaces that optimize the configuration of the interface for specific tasks. The <a class="twikiLink" href="/twiki/bin/view/MouseBIRN/MBAT">MBAT</a> Startup Page points the user to the various Workspaces. The quicklinks offered from the Startup Page include Search by Region of Interest, Query Data, Open Data, View Atlas and Create Atlas. 
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<h4><a name="REFERENCES_FOR_MBAT"> </a><a name="REFERENCES_FOR_MBAT_"> </a> REFERENCES FOR <a class="twikiLink" href="/twiki/bin/view/MouseBIRN/MBAT">MBAT</a>: </h4>
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<li> Boline JK, <a class="twikiLink" href="/twiki/bin/view/MouseBIRN/MacKenzie">MacKenzie</a>-Graham A, Shattuck D, Yuan H, Anderson S, Sforza DM, Wang J, Williams RW, Wong W, Martone ME, Zaslavsky I, Toga AW (2006)  A Digital Atlas and Neuroinformatics Framework for Query and Display of Disparate Data.  Society for Neuroscience, Abstract #100.12
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<li> <a class="twikiLink" href="/twiki/bin/view/MouseBIRN/MacKenzie">MacKenzie</a>-Graham, A., Tinsley, M.R., Shah, K.P., Aguilar, C., Strickland, L.V., Boline, J., Martin, M., Morales, L., Shattuck, D.W., Jacobs, R.E., Voskuhl, R.R., and Toga, A.W.  (2006)  Cerebellar Cortical Atrophy in Experimental Autoimmune Encephalomyelitis.  Neuroimage, 32(3):1016-23.
</li>

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<h3><a name="DOWNLOAD_MBAT"> </a><a name="DOWNLOAD_MBAT_"> </a> DOWNLOAD <a class="twikiLink" href="/twiki/bin/view/MouseBIRN/MBAT">MBAT</a>: </h3>
RELEASE DATE: 11/07. The Mouse BIRN is pleased to announce a beta version 2.0 release of the Mouse BIRN Atlasing Toolkit(<a class="twikiLink" href="/twiki/bin/view/MouseBIRN/MBAT">MBAT</a>).  This version may be downloaded from the <a href="http://nbirn.net/tools/mbat/index.shtm" target="_top">BIRN site</a>, or on the <a href="http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=29" target="_top">LONI site</a>.  Contact <a href="mailto:jyl.boline@loni.ucla.edu">Jyl Boline</a>.  

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To download the full <a class="twikiLink" href="/twiki/bin/view/MouseBIRN/MBAT">MBAT</a> package, visit the <a href="http://nbirn.net/tools/mbat/index.shtm" target="_top">BIRN downloads</a> page
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<li> <a href="http://www.loni.ucla.edu/twiki/pub/MouseBIRN/MBAT/MBAT training.ppt" target="_top">Training Powerpoint</a>: Powerpoint presentation of key <a class="twikiLink" href="/twiki/bin/view/MouseBIRN/MBAT">MBAT</a> features and usage
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<li> <a href="http://www.loni.ucla.edu/twiki/pub/MouseBIRN/MBAT_v110/MBAT_v1.1_beta_tutorial.pdf" target="_top">MBAT_v2.0_beta_tutorial.pdf</a>: Users Guide
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<li> <a href="http://cms.loni.ucla.edu/mbat/support.aspx?id=3430" target="_top">FAQ</a>: Frequently Asked Questions
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<li> <a href="http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=29" target="_top">MBAT_release.zip</a>: <a class="twikiLink" href="/twiki/bin/view/MouseBIRN/MBAT">MBAT</a> program
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Download the Atlases and Data zip files and place the Atlases and Volume folders in your <a class="twikiLink" href="/twiki/bin/view/MouseBIRN/MBAT">MBAT</a> folder for additional atlases and data.
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<li> <a href="http://www.nbirn.net/bdr/mouse_mda/index.shtm" target="_top">MDA</a>: Additional atlases for visualization in <a class="twikiLink" href="/twiki/bin/view/MouseBIRN/MBAT">MBAT</a>
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<h3><a name="https_cms_loni_ucla_edu_MBAT_for"> </a><a name="_https_cms_loni_ucla_edu_MBAT_fo"> </a> <a href="https://cms.loni.ucla.edu/MBAT/forum.aspx" target="_top">VISIT the MBAT Forum:</a> </h3>

A forum space for users to ask questions, report bugs, and make comments and suggestions.
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<h3><a name="MouseBIRNProgrammers_VISIT_the_M"> </a><a name="_MouseBIRNProgrammers_VISIT_the_"> </a> <a class="twikiLink" href="/twiki/bin/view/MouseBIRN/MouseBIRNProgrammers">VISIT the MBAT Programmers Page:</a> </h3>
A space for additional technical information about <a class="twikiLink" href="/twiki/bin/view/MouseBIRN/MBAT">MBAT</a> 
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Link to the Older version of <a class="twikiLink" href="/twiki/bin/view/MouseBIRN/MBAT">MBAT</a>: 
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<li> <a class="twikiLink" href="/twiki/bin/view/MouseBIRN/MBAT_v150">MBAT 1.1.5 beta, released May 2007</a>
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<li> <a class="twikiLink" href="/twiki/bin/view/MouseBIRN/MBAT_v110">MBAT 1.1.0 beta, released November 2006</a> 
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<li> <a class="twikiLink" href="/twiki/bin/view/MouseBIRN/MBAT_v1">MBAT 1.0.0 beta, released October 2006</a>
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<tr><th class="twikiFirstCol" bgcolor="#99CCCC"><a class="twikiLink" href="/twiki/bin/view/TWiki/FileAttachment">Attachment</a> <a href="http://www.loni.ucla.edu/twiki/bin/view/MouseBIRN/MBAT?rev=1.21&amp;sortcol=0&amp;table=1&amp;up=0#sorted_table" title="Sort by this column"><img src="http://www.loni.ucla.edu/twiki/pub/TWiki/TablePlugin/diamond.gif" border="0" alt="sort" /></a></th><th bgcolor="#99CCCC"><a href="http://www.loni.ucla.edu/twiki/bin/view/MouseBIRN/MBAT?rev=1.21&amp;sortcol=1&amp;table=1&amp;up=0#sorted_table" title="Sort by this column"> Action</a> </th><th bgcolor="#99CCCC"><a href="http://www.loni.ucla.edu/twiki/bin/view/MouseBIRN/MBAT?rev=1.21&amp;sortcol=2&amp;table=1&amp;up=0#sorted_table" title="Sort by this column"> Size</a> </th><th bgcolor="#99CCCC"><a href="http://www.loni.ucla.edu/twiki/bin/view/MouseBIRN/MBAT?rev=1.21&amp;sortcol=3&amp;table=1&amp;up=0#sorted_table" title="Sort by this column"> Date</a> </th><th bgcolor="#99CCCC"><a href="http://www.loni.ucla.edu/twiki/bin/view/MouseBIRN/MBAT?rev=1.21&amp;sortcol=4&amp;table=1&amp;up=0#sorted_table" title="Sort by this column"> Who</a> </th><th bgcolor="#99CCCC"><a href="http://www.loni.ucla.edu/twiki/bin/view/MouseBIRN/MBAT?rev=1.21&amp;sortcol=5&amp;table=1&amp;up=0#sorted_table" title="Sort by this column"> Comment</a> </th></tr>

<tr><td class="twikiFirstCol" bgcolor="#FFFFFF"> <img src="/twiki/pub/icn/ppt.gif" width="16" height="16" align="top" alt="" border="0" /> <a href="/twiki/pub/MouseBIRN/MBAT/MBATtraining.ppt">MBATtraining.ppt</a> </td><td bgcolor="#FFFFFF"> <a href="http://www.loni.ucla.edu/twiki/bin/attach/MouseBIRN/MBAT?filename=MBATtraining.ppt&amp;revInfo=1" title="change, update, previous revisions, move, delete...">manage</a> </td><td align="right" bgcolor="#FFFFFF"> 7112.5&nbsp;K </td><td bgcolor="#FFFFFF"> 30 Nov 2007 - 18:47 </td><td bgcolor="#FFFFFF"> <a class="twikiLink" href="/twiki/bin/view/Main/QueenieNg">QueenieNg</a> </td><td bgcolor="#FFFFFF"> <a class="twikiLink" href="/twiki/bin/view/MouseBIRN/MBAT">MBAT</a> Training Powerpoint </td></tr>

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