1. view and compare different types of data that is spatially registered to the atlas

In Maryann's document, she lists several potential user workflows. I've tried to separate them into different functions:

Visualization/gross comparisons of atlases or their own data:

1. access a free brain atlas to learn about brain anatomy
2. compare different methods of visualizing brain structure, e.g., Nissl, MRI, DTI imaging
3. view and manipulate individual 2D images or 3D volumes, e.g., reslice

Adding data to mouse BIRN interface for comparison purposes:

1. spatially register their data to the brain atlas
2. compare their own data against that of the atlas (additional comparison methods added below in the analysis/quantification section)
3. Add their data to the BIRN data resources

Mine/query atlases for related information:

1. use the brain atlas interface to retrieve data indexed to a particular location, e.g., EM data sets
2. use the brain atlas interface to examine patterns of gene expression

1. retrieve data linked to spatial location or ontology:
   1. higher resolution images (i.e. EM, other microscopy)
   2. images with additional information than spatial (i.e. gene expression)
   3. publications on that area (perhaps with the ability to combine with genes expressed there, or with disease model, etc.)
   4. other text based information (i.e. BAMS etc)

Analysis and quantification:

1. tools to measure signal intensities (like what SmartAtlas^? does now)
2. tools to delineate their own images
3. tools for volumetric comparisons between chosen images, atlases, or populations
4. tools for measuring certain parts of images (i.e. volumes, distances, thicknesses, etc)
5. tools for statistical comparisons or perhaps just output of a file that could be used in other programs

These functional workflows suggest different "modes" of the user that may or may not be reflected in the interface:

1. viewing mode
2. simple query mode
3. advanced query mode
4. register new image to atlas mode
   1. delineate/analyze new image
   2. quantification of new image
   3. compare new image to atlas (something like an atlas overlay?)

Available atlases

When talking about atlases that are available to us, it seems there are two main subdivision of atlases that may greatly affect our effort. Comments or others?

1. based on who did the delineations and annotations
2. not just 2D vs. 3D, but actually on the image type