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)

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