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.

5) Java 1.4.2 and 1.5 as well on Unix and windows.

6) No API.