MouseBIRNScientificCommunity < MouseBIRN

---+++++Please see [[http://www.loni.ucla.edu/twiki/bin/view/MouseBIRN/MouseBIRNResources][Mouse BIRN Resources]] to access the resources shared by Mouse BIRN.  

The mouse BIRN is a research and development effort that will result in a distributed adaptive database and multiscale, multimodality atlases of the mouse brain. Tools to incorporate and compare data from gene expression patterns to gross morphology from multiple laboratories at scales from nanometers to centimeters will be built.  This is an effort to integrate data already existing or to be generated as part of this or other NIH-wide or privately funded programs.


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Developed resources (e.g., software, software documentation, source codes, data sets, calibration standards, correction models, etc.) will be posted for the scientific community to access and use as desired through the BIRN web site and portal. 

*Deliverables:* 
   * Development and testing of methods and best practices for data collection and management
      * Experimental/collection methods for the data types used in this group
      * Data acquisition formats and conversions
      * Data storage and access
      * Data sharing policies and security 
  

   * Tools and documentation of how to use 
      * All tools generated in mouse BIRN effort will be free to the public
      * Demos/tutorials
      * Many will be open source when appropriate


   * Access to protocols and pipelines for processing various data types
      * MRI 3D volumes (i.e., T1, T2, DTI, MRH)
      * 2D slices (i.e., blockface imaging, Nissl-stain, gene expression maps)
      * Cell level (i.e. confocal, multiphoton microscopy)
      * Subcellular (i.e. electron tomography)
      * Microarray(?)


   * Protocols and pipelines for atlasing data:
      * MRI 3D volumes
      * 2D slices 
      * Cellular
      * Subcellular


   * Protocols and pipelines for analyzing data
      * MRI atlases:  i.e. examine volumes of areas and compare to atlases of other populations
      * Protein/RNA expression:  i.e. examine amount of expression shown in an area of interest
      * Automated segmentation:  (farther down the road)


   * All data once in the mouse BIRN databases will be accessible to the public
      * Atlased data:
         * Data generated by mouse BIRN
         * Some GENSAT data 
      * Text-based information such as nomenclature, descriptions of gene expression, literature citations, and data derived from microarrays associated with an anatomical region or one defined by functional criteria.


   * Querying this data:
      * Once the data is in the same space as the atlas, researchers will be able to make comparisons between it and the atlas, across their own data, or with data acquired in other laboratories.
         * Spatial
         * Ontologies
         * Semantic (some relation to UMLS)
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