AtlasStateExchange < MouseBIRN

---++++Things to do here:
   *  a) we will send the API and demos around
   *  b) review the API and demo communications, to see if it will fit your atlas (Willy and Joshua will help with this)
   *  c) review the current representation of "atlas state", to see if it is general enough
   *  d) formally describe spatial reference systems we use: e.g. Stereotaxic1 (used at UCLA), Stereotaxic2 (used in UCSD atlas), image1 (used at Drexel)
   *  e) define transformations between all coordinate systems, and some canonical stareotaxic system (either Stereotaxic1 or 2)
   *  f) create services for converting between the coordinate systems (though for a limited number of coordinate systems just sharing conversion code fragments would be more robust). It is straightforward for some conversions; may be pretty involved when converting from image to stereotaxic. For the latter, we need to have a couple test cases
   *  g) create services for format conversion: i.e. between polygons specified as coordinate pairs or triplets, and collections of pixels/voxels (Bill mentioned that they may have appropriate code at Drexel).

Now with respect to ontology - the "semantic reference system" may be handled in a similar way: i.e. when giving a name of a feature must also
specify the ontology in which it lives.

2. Ability to search registered images/volumes/segmentations available in other atlases.
   *  a) UCSD will send the schema of our spatial registry source
   *  b) we need to see how to register 3D volumes and 2D images to such or similar source (using Drexel's alignment/warping tools?), so that the metadata sources can be searched in uniform way.

3. Ability to load images / slices / segmentations into any atlas.
   *  a) UCSD will provide sample code for retrieving image fragments from <verbatim>ArcIMS</verbatim>
   *  b) UCSD will develop a web service to return feature coordinates (as polygon boundary, as well as label point) given the feature name and set of slices
   *  c) let's go first through a manual process of loading each other's images.



---++++Syntax for Atlas Interoperation
http://imhotep.ucsd.edu:7873/trantj/mouse_birn/newXMLFormat.htm
---
---++++Examples of Syntax and XML schemas for atlas state exchange (as of 6/28/2005)

   * [[%ATTACHURL%/state_init.xsd][state_init.xsd]]: initilize

   * [[%ATTACHURL%/state_submit.xsd][state_submit.xsd]]: Submit

   * [[%ATTACHURL%/state_retrieve.xsd][state_retrieve.xsd]]: Retrieve

   * [[%ATTACHURL%/state_end.xsd][state_end.xsd]]: End

   * [[%ATTACHURL%/state_init.xml][state_init.xml]]: Example atlas_state init message

   * [[%ATTACHURL%/state_submit.xml][state_submit.xml]]: Example atlas_state submit message

   * [[%ATTACHURL%/state_retrieve.xml][state_retrieve.xml]]: Example atlas_state retieve message

   * [[%ATTACHURL%/state_end.xml][state_end.xml]]: Example atlas_state end message

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---+++++Continued Work can be found at [[AtlasStateExchange_2007][the 2007 wiki page for Atlas State Exchange]]
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