Things to do here:

Syntax for Atlas Interoperation

Examples of Syntax and XML schemas for atlas state exchange (as of 6/28/2005)

Continued Work can be found at the 2007 wiki page for Atlas State Exchange

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 ArcIMS
• 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

• state_init.xsd: initilize

• state_submit.xsd: Submit

• state_retrieve.xsd: Retrieve

• state_end.xsd: End

• state_init.xml: Example atlas_state init message

• state_submit.xml: Example atlas_state submit message

• state_retrieve.xml: Example atlas_state retieve message

• state_end.xml: Example atlas_state end message