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ABOUT THE MOUSE BIRN ATLASING TOOLKIT (MBAT)
GENERAL DESCRIPTION:
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This is a collaborative effort by the groups of the Mouse BIRN to create an interoperable tool that offers an intuitive way to access the functionality offered by the individual efforts. The goal of the MBAT 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 1.1.5 beta, release May 2007
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Version: MBAT 2.0 beta, release November 2007
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Report Bugs at The BIRN help page, or at the MBAT forum
- MBAT.jpg:
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Report Bugs at The BIRN help page, or MBAT forum of the official LONI MBAT Website
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FEATURES:
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- DATA VOLUMES
- This version includes the option to download several different data volumes created by the Mouse BIRN group for visualization. Most of the data volumes are Analyze image 7.5 format. However, it is possible to load several other types of images into the main viewer. These datasets can be downloaded from the BIRN site or here.
- ATLASES
- It is packaged with 3 different atlas delineations: one based on Swanson 1998, another one on Paxinos 2001, and one on Swanson 2004 and Paxinos and Franklin 2001. Some of these atlases also include 3D surfaces that can be viewed with the 3D viewer and Surface Manager, and the structural hierarchies can be viewed and navigated using BrainGraph tool.
- QUERY DATA
- A major goal of this tool is to provide access to remote databases for querying and viewing multiscale data.
- Expression query tool
- This tool queries microarray gene expression data from different databases. This includes the GeneNetwork database and the BIRN Microarray database. The return of the query is shown as color values corresponding to gene expression levels for some areas of the brain. Movie demonstrating GeneNetwork query tool Microarray data upload tutorial document or See the flash tutorial here. From this interface it is also possible to query and view the high resolution cell fills and brain maps from the CCDB. Right click on the anatomical structure in the query return to launch this.
HIGHLIGHTS:
- BrainGraph
- This version of BrainGraph tool adds colored label nodes which correspond to the label volume and label index to make it more visually enriched and easily identify and navigate the brain structures. Also, the new tree view option provides clearer and organized hierarchical information of structures to view the brain.
- FlexDock
- FlexDock gives users the flexibility to dock multiple windows dynamically. Users can now view the data all at once without switching back and forth different windows.
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- DATA QUERIES
- 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.
- Concept-based Queries
- 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 MBAT. For those that cannot, a link to an external website may be provided.
- Spatial-based Queries
- 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.
- EM/Cell Queries
- High resolution cell fills and brain maps spatially linked to the MBAT atlases can be located, viewed, and downloaded. This query tool accesses the database at CCDB.
- Expression Queries
- Expression queries allow the user to search for microarray gene expression data from different databases. This includes the GeneNetwork database http://www.genenetwork.org]] and the BIRN Microarray database http://microarray.nbirn.net/index.html]]. The return of the query is shown as color values corresponding to gene expression levels for some areas of the brain.
- ATLASES
- MBAT 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 MBAT 3D Viewer and Surface Manager, and a structural hierarchy that can be viewed and navigated through using the BrainGraph tool. Several additional atlas delinations are available for download at http://www.nbirn.net/bdr/bdr_current_data.shtm.
- DATA VOLUMES
- MBAT 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 MBAT viewer. These datasets can be found on the BIRN download site BIRN site or here.
- BrainGraph
- BrainGraph 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 BrainGraph editor has been integrated into the MBAT application. BrainGraph 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.
- Workspaces
- MBAT offers different Workspaces that optimize the configuration of the interface for specific tasks. The MBAT 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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REFERENCES FOR MBAT:
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Boline JK, MacKenzie-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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- Boline JK, MacKenzie-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
- MacKenzie-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.
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DOWNLOAD MBAT:
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RELEASE DATE: 05/07. The Mouse BIRN is pleased to announce a beta version 1.1.5 release of the Mouse BIRN Atlasing Toolkit(MBAT). This version may be downloaded from the BIRN site, or on the LONI site. Contact Jyl Boline.
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RELEASE DATE: 11/07. The Mouse BIRN is pleased to announce a beta version 2.0 release of the Mouse BIRN Atlasing Toolkit(MBAT). This version may be downloaded from the BIRN site, or on the LONI site. Contact Jyl Boline.
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To download the full MBAT package, visit the BIRN downloads page
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To download the full MBAT package, visit the BIRN downloads page
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Download the Atlases and Data zip files and place the Atlases and Volume folders in your MBAT folder for additional atlases and data.
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- MDA: Additional atlases for visualization in MBAT
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A forum space for users to ask questions, report bugs, and make comments and suggestions.
A space for additional technical information about MBAT
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MBAT Design Page
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Link to the Older version of MBAT: MBAT 1.1.0 beta, released November 2007 and MBAT 1.0.0 beta, released October 2006
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Link to the Older version of MBAT:
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| META FILEATTACHMENT | MBAT.jpg | attr="" comment="" date="1160691999" path="MBAT.jpg" size="59337" user="mouseBIRN" version="1.3" |
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| META FILEATTACHMENT | MBAT.JPG | attr="h" comment="" date="1160691835" path="MBAT.JPG" size="59337" user="mouseBIRN" version="1.1" |
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| META FILEATTACHMENT | MBATreadme.txt | attr="" comment="MBAT v1.1 Beta Readme File" date="1160704816" path="MBATreadme.txt" size="490" user="jboline" version="1.1" |
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| META FILEATTACHMENT | birn_uad_tutorial.pdf | attr="" comment="Microarray Data upload tutorial" date="1171072123" path="C:\Documents and Settings\qng\My Documents\BIRN\Bret data\tutorial\birn_uad_tutorial.pdf" size="482564" user="qng" version="1.1" |
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| META FILEATTACHMENT | MBAT_release.zip | attr="" comment="MBAT program zipped" date="1179937714" path="MBAT_release.zip" size="6778774" user="jboline" version="1.1" |
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| META FILEATTACHMENT | mbat20.jpg | attr="h" comment="MBAT 2.0 screen shot" date="1196448321" path="C:\Documents and Settings\qng\My Documents\BIRN\Mouse BIRN\MBAT\doc\figures\mbat20.jpg" size="3346" user="qng" version="1.1" |
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| META FILEATTACHMENT | MBATtraining.ppt | attr="" comment="MBAT Training Powerpoint" date="1196448450" path="C:\Documents and Settings\qng\My Documents\BIRN\Mouse BIRN\MBAT\doc\MBAT training.ppt" size="7283200" user="qng" version="1.1" |
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| META FILEATTACHMENT | mbat20b.jpg | attr="" comment="MBAT 2.0 screen shot" date="1196448920" path="C:\Documents and Settings\qng\My Documents\BIRN\Mouse BIRN\MBAT\doc\figures\mbat20b.jpg" size="68798" user="qng" version="1.1" |
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| META FILEATTACHMENT | MBAT_home_1.jpg | attr="" comment="" date="1196449824" path="C:\Documents and Settings\qng\My Documents\BIRN\Mouse BIRN\MBAT\doc\figures\MBAT_home_1.jpg" size="5846" user="qng" version="1.1" |
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| META FILEATTACHMENT | MBAT_home_2.gif | attr="h" comment="" date="1196449847" path="C:\Documents and Settings\qng\My Documents\BIRN\Mouse BIRN\MBAT\doc\figures\MBAT_home_2.gif" size="6778" user="qng" version="1.1" |
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| META FILEATTACHMENT | MBAT_home_3.jpg | attr="h" comment="" date="1196449874" path="C:\Documents and Settings\qng\My Documents\BIRN\Mouse BIRN\MBAT\doc\figures\MBAT_home_3.jpg" size="5108" user="qng" version="1.1" |
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| META FILEATTACHMENT | MBAT_home_4.jpg | attr="h" comment="" date="1196449906" path="C:\Documents and Settings\qng\My Documents\BIRN\Mouse BIRN\MBAT\doc\figures\MBAT_home_4.jpg" size="6641" user="qng" version="1.1" |
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ABOUT THE MOUSE BIRN ATLASING TOOLKIT (MBAT)
GENERAL DESCRIPTION:
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This is a collaborative effort by the groups of the Mouse BIRN to create an interoperable tool that offers an intuitive way to access the functionality offered by the individual efforts. The goal of the MBAT 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 1.1.0 beta
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Version: MBAT 1.1.5 beta, release May 2007
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Report Bugs at http://bugzilla.nbirn.net/bugzilla/enter_bug.cgi. You must have an account on this site
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Report Bugs at The BIRN help page, or at the MBAT forum
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- MBAT.jpg:
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- DATA VOLUMES
- This version includes the option to download several different data volumes created by the Mouse BIRN group for visualization. Most of the data volumes are Analyze image 7.5 format. However, it is possible to load several other types of images into the main viewer. These datasets can be downloaded from the BIRN site or here.
- ATLASES
- It is packaged with 3 different atlas delineations: one based on Swanson 1998, another one on Paxinos 2001, and one on Swanson 2004 and Paxinos and Franklin 2001. Some of these atlases also include 3D surfaces that can be viewed with the 3D viewer and Surface Manager, and the structural hierarchies can be viewed and navigated using BrainGraph tool.
- QUERY DATA
- A major goal of this tool is to provide access to remote databases for querying and viewing multiscale data.
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<
< |
-
- EM/Cell query tool
- High resolution cell fills and brain maps spatially linked to the MBAT atlases can be located, viewed, and downloaded through this tool. This tool accesses the database at http://ccdb.ucsd.edu/CCDBWebSite/index.html. Movie demonstrating CCDB query tool
- Expression query tool
- This tool queries microarray gene expression data from different databases including the GeneNetwork database (http://www.genenetwork.org) and Microarray database (http://132.239.131.189/birn_uad/). The return of the query is shown as color values corresponding to gene expression levels for some areas of the brain. Movie demonstrating GeneNetwork query tool Microarray data upload tutorial document or See the flash tutorial here
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-
- Expression query tool
- This tool queries microarray gene expression data from different databases. This includes the GeneNetwork database and the BIRN Microarray database. The return of the query is shown as color values corresponding to gene expression levels for some areas of the brain. Movie demonstrating GeneNetwork query tool Microarray data upload tutorial document or See the flash tutorial here. From this interface it is also possible to query and view the high resolution cell fills and brain maps from the CCDB. Right click on the anatomical structure in the query return to launch this.
|
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HIGHLIGHTS:
- BrainGraph
- This version of BrainGraph tool adds colored label nodes which correspond to the label volume and label index to make it more visually enriched and easily 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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<
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- FlexDock
- FlexDock is new to this version. It gives users the flexibility to dock multiple windows dynamically. Users can now view the data all at once without switching back and forth different windows.
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- FlexDock
- FlexDock gives users the flexibility to dock multiple windows dynamically. Users can now view the data all at once without switching back and forth different windows.
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DOWNLOAD MBAT:
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RELEASE DATE: 10/16/06. The Mouse BIRN is pleased to announce a beta version 1.1.0 release of the Mouse BIRN Atlasing Toolkit(MBAT). This version may be downloaded from the BIRN site, or on the LONI site. Contact Jyl Boline.
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RELEASE DATE: 05/07. The Mouse BIRN is pleased to announce a beta version 1.1.5 release of the Mouse BIRN Atlasing Toolkit(MBAT). This version may be downloaded from the BIRN site, or on the LONI site. Contact Jyl Boline.
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To download the full MBAT package, visit the BIRN downloads page
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ABOUT THE MOUSE BIRN ATLASING TOOLKIT (MBAT)
GENERAL DESCRIPTION:
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DOWNLOAD MBAT:
RELEASE DATE: 10/16/06. The Mouse BIRN is pleased to announce a beta version 1.1.0 release of the Mouse BIRN Atlasing Toolkit(MBAT). This version may be downloaded from the BIRN site, or on the LONI site. Contact Jyl Boline.
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To download the full MBAT package, visit the BIRN downloads page
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Download the Atlases and Data zip files and place the Atlases and Volume folders in your MBAT folder for additional atlases and data.
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| META FILEATTACHMENT | MBAT.jpg | attr="" comment="" date="1160691999" path="MBAT.jpg" size="59337" user="mouseBIRN" version="1.3" |
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| META FILEATTACHMENT | MBAT.JPG | attr="h" comment="" date="1160691835" path="MBAT.JPG" size="59337" user="mouseBIRN" version="1.1" |
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| META FILEATTACHMENT | MBATdata.zip | attr="" comment="Additional data for display in MBAT" date="1160704682" path="MBATdata.zip" size="12076217" user="jboline" version="1.1" |
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| META FILEATTACHMENT | MBAT_v1.1Beta_tutorial.pdf | attr="" comment="MBAT v1.1 Beta Tutorial" date="1160704718" path="MBAT_v1.1Beta_tutorial.pdf" size="3264761" user="jboline" version="1.1" |
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| META FILEATTACHMENT | MBATreadme.txt | attr="" comment="MBAT v1.1 Beta Readme File" date="1160704816" path="MBATreadme.txt" size="490" user="jboline" version="1.1" |
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| META FILEATTACHMENT | MBAT.zip | attr="" comment="MBAT installation zip file" date="1160931880" path="MBAT.zip" size="21521131" user="jboline" version="1.1" |
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| META FILEATTACHMENT | MBAT_Atlases.zip | attr="" comment="Additional atlases for visualization in MBAT" date="1160934983" path="MBAT_Atlases.zip" size="16063541" user="jboline" version="1.1" |
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| META FILEATTACHMENT | MBAT_small.zip | attr="" comment="Minimal installation of MBAT-no 3D surfaces" date="1161019312" path="MBAT_small.zip" size="21520516" user="jboline" version="1.1" |
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| META FILEATTACHMENT | MBAT_small.zip | attr="" comment="Minimal installation of MBAT-no 3D surfaces" date="1161028852" path="MBAT_small.zip" size="21422841" user="jboline" version="1.2" |
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| META FILEATTACHMENT | MBAT_v1.1_beta_tutorial.pdf | attr="" comment="Users documentation" date="1161029163" path="MBAT_v1.1_beta_tutorial.pdf" size="3096974" user="jboline" version="1.1" |
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ABOUT THE MOUSE BIRN ATLASING TOOLKIT (MBAT)
General Description
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ABOUT THE MOUSE BIRN ATLASING TOOLKIT (MBAT)
GENERAL DESCRIPTION:
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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.
This is a collaborative effort by the groups of the Mouse BIRN to create an interoperable tool that offers an intuitive way to access the functionality offered by the individual efforts. The goal of the MBAT 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.
Version: MBAT 1.1.0 beta
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Older version: MBAT 1.0.0 beta
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Report Bugs at http://bugzilla.nbirn.net/bugzilla/enter_bug.cgi. You must have an account on this site
- MBAT.jpg:
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Features
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FEATURES:
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- DATA VOLUMES
- This version includes the option to download several different data volumes created by the Mouse BIRN group for visualization. Most of the data volumes are Analyze image 7.5 format. However, it is possible to load several other types of images into the main viewer. These datasets can be downloaded from the BIRN site or here.
- ATLASES
- It is packaged with 3 different atlas delineations: one based on Swanson 1998, another one on Paxinos 2001, and one on Swanson 2004 and Paxinos and Franklin 2001. Some of these atlases also include 3D surfaces that can be viewed with the 3D viewer and Surface Manager, and the structural hierarchies can be viewed and navigated using BrainGraph tool.
- QUERY DATA
- A major goal of this tool is to provide access to remote databases for querying and viewing multiscale data.
- EM/Cell query tool
- High resolution cell fills and brain maps spatially linked to the MBAT atlases can be located, viewed, and downloaded through this tool. This tool accesses the database at http://ccdb.ucsd.edu/CCDBWebSite/index.html. Movie demonstrating CCDB query tool
- Expression query tool
- This tool queries microarray gene expression data from different databases including the GeneNetwork database (http://www.genenetwork.org) and Microarray database (http://birn.ncrr.nih.gov/brin_uad/). The return of the query is shown as color values corresponding to gene expression levels for some areas of the brain. Movie demonstrating GeneNetwork query tool
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Highlights
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HIGHLIGHTS:
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- BrainGraph
- This version of BrainGraph tool adds colored label nodes which correspond to the label volume and label index to make it more visually enriched and easily identify and navigate the brain structures. Also, the new tree view option provides clearer and organized hierarchical information of structures to view the brain.
- FlexDock
- FlexDock is new to this version. It gives users the flexibility to dock multiple windows dynamically. Users can now view the data all at once without switching back and forth different windows.
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DOWNLOAD MBAT
RELEASE DATE: 10/13/06. The Mouse BIRN is pleased to announce a beta version 1.1.0 release of the Mouse BIRN Atlasing Toolkit(MBAT). This version may be downloaded from the BIRN site, or on the LONI site. Contact Jyl Boline.
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>
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DOWNLOAD MBAT:
RELEASE DATE: 10/16/06. The Mouse BIRN is pleased to announce a beta version 1.1.0 release of the Mouse BIRN Atlasing Toolkit(MBAT). This version may be downloaded from the BIRN site, or on the LONI site. Contact Jyl Boline.
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>
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Download the Atlases and Data zip files and place the Atlases and Volume folders in your MBAT folder for additional atlases and data.
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Link to the Older version of MBAT: MBAT 1.0.0 beta
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| META FILEATTACHMENT | MBATdata.zip | attr="" comment="Additional data for display in MBAT" date="1160704682" path="MBATdata.zip" size="12076217" user="jboline" version="1.1" |
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| META FILEATTACHMENT | MBAT_v1.1Beta_tutorial.pdf | attr="" comment="MBAT v1.1 Beta Tutorial" date="1160704718" path="MBAT_v1.1Beta_tutorial.pdf" size="3264761" user="jboline" version="1.1" |
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| META FILEATTACHMENT | MBATreadme.txt | attr="" comment="MBAT v1.1 Beta Readme File" date="1160704816" path="MBATreadme.txt" size="490" user="jboline" version="1.1" |
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| META FILEATTACHMENT | MBAT.zip | attr="" comment="MBAT installation zip file" date="1160931880" path="MBAT.zip" size="21521131" user="jboline" version="1.1" |
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| META FILEATTACHMENT | MBAT_Atlases.zip | attr="" comment="Additional atlases for visualization in MBAT" date="1160934983" path="MBAT_Atlases.zip" size="16063541" user="jboline" version="1.1" |
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