• Link to Temporary Mouse BIRN Portal

• • This program can be found on the BIRN Portal at /home/Public/MouseBIRN_Publicdata/MBAT. It is offered as a .zip package, a .tgz package, or simply download the whole MBAT program folder.

• Exchange of state between atlases Page

• Common Data Models Working Pages

• MBAT Work Page

Atlas Related Working Pages

MBAT Work Page

Structure Hierarchy Working Page

Collaborative Atlas Working Page

Atlas Planning and Action Items

Atlasing workshop day at the BIRN AHM (10/26/05)

Atlas Plan and Action Items generated at June 2005 mouse AHM:

Atlas workgroup meetings dealing with biological aspects of atlasing

• 2006_3_08_atlasingissues.doc: Minutes from atlasing WG discussion of structure hierarchy and online collaborative atlas building

Link to Temporary Mouse BIRN Portal

Download beta version of the Mouse BIRN Atlasing Toolkit (MBAT) (11/18/05)

Use Cases

• AtlasIntegrationScenarios.doc: Expanded version of Mouse BIRN atlas integration scenario

UseCaseWorkPage

AtlasWishList

FeaturesFromRelatedPrograms

Atlas integration notes and task list:

Exchange of state between atlases:

Site specific information on their Atlasing Tools

Atlas Planning and Action Items

Structure Hierarchy Working Page

1. Exchange of state between atlases:

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

Defining "atlas"

1. Where can you access your atlas/program?
2. What coordinate system does your atlas use?
3. What terminology do you use to map your data?
4. What types and formats of data does your program read?
5. What language is it written in and for which platforms?
6. Does your program have a formal API?

UCSD

1. You can launch the SmartAtlas by Java WebStart (Java compiler required , 1.4 or above preferred) at http://imhotep.ucsd.edu:7873/smart_atlas_annotation/Testing.htm

2. Stereotaxic coordinate system (as in Paxinos, Franklin): in front of/behind bregma -- ventral/dorsal to bregma -- lateral to midline On coronal slices: the first coordinate is constant; the second coordinate increases downward, the third coordinate changes from -5 to +5, from left to right.

3. Paxinos labels, mapped where possible to UMLS concept ids and Neuronames

4. Currently reads image files(jpg, tiff,...etc) served by ArcIMS image server and SRB. Also reads vector data (shapefiles), either from files or as binary streams served by ArcIMS feature service.

5. Java 1.4.2 for Unix and Windows

6. No formal API yet, though many elements are accessible: e.g. there is a standard language to query ArcIMS data services; access data in SRB; start the Atlas from a pre-defined state, etc.

Drexel

UCLA

1) It can be downloaded from the LONI site at http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=12., it is a stand alone application.

2) SHIVA doesn't automatically put the files into a coordinate system per se., we're working on defining the start points and such so that it will display coordinates. We are working on using the Paxinos bregma coordinate frame as a reference.

3) Theoretically it can be multiple ones but we'll focus on Paxinos and Swanson from BAMS.

4) Primarily Analyze Image, Minc, TIFF (simple), with a couple proprietary data formats (i.e. CIT, Duke). Plus there are some specific files for the atlas, including .keg (coordination file) and .lbl (label lookup table) files.

Atlas Plan and Action Items generated at June 2005 mouse AHM:

• a) UCSD will provide sample code for retrieving image fragments from ArcIMS^?

• MouseBrainEnvironment.html: A mouse brain study environment

What coordinate system does your atlas use?

What terminology do you use to map your data?

What types and formats of data does your program read?

What language is it written in and for which platforms?

Does your program have a formal API?

Use Cases

• AtlasIntegrationScenarios.doc: Expanded version of Mouse BIRN atlas integration scenario

Use Cases

• AtlasIntegrationScenarios.doc: Some brief notes and thoughts on possible use cases, with heavy emphasis on gene expression data