A mouse brain environment
Should have
- a system of coordinates which can be related to a reference coordinate system (Paxinos & Franklin)
- a reference atlas or brain image
- a map: a labeled atlas or brain image (closed contours corresponding to neuroanatomical structures)
- a way to compare a particular data set to the atlas (side by side scrolling or overlay)
- a relatively simple built-in CNS ontology hierarchical search tool such as the "Expression Pattern Search" builit into Genepaint.org (
http://www.genepaint.org)
Can have (static) information
- animal: species, strain, ID, age, sex, weight, behavioral and/or anatomical and/or physiological phenotype, normal or wild type or control vs model of disease (stage of disease, phenotype), in vivo versuss ex vivo, animal preparation, whole or part imaged
- image modality
-acquisition parameters or staining
-resolution in plane between planes
-location: plane orientation and position, position in plane
-image intensity and or corresponding parameters (T1,T2, cell density, receptor density, uptake)
-image preprocessing if any (registered, scaled, intensity normalized , parametric map ...)
-associated with other images (for multimodality studies) or with different postprocessing (labeling, etc)
-which labels & synonyms(latin &english name) (ontology)
-rater or labeler (in case there are multiple people processing data in the same way) so interrater analysis can be done
Can provide (dynamic) information
- all images associated with the current one (for multimodality studies) or postprocessing (labeling)
- location and parameters of a point selected by the user
- see same region in some other or in all images associated with the current one
- simultaneous viewing in different windows and /or overlay
- parameters of other images at the same location
- measure distances
- measure SNR, CNR
- label at this location, cell type(s) in label, involvement of structure in normal physiological activity or in disease, volume, variability, connectivity (visualize system), extent
- analysis & studies done on this particular brain
- planar, 3D view
- overlay atlas with current data set
- overlay two data sets
