Coordinate Systems
Atlases
The table below describes the coordinate systems of the reference atlases distributed in Cell Locator.
Reference atlas |
Atlas Version |
Coordinate System Dimensions |
---|---|---|
Allen Mouse Brain Common Coordinate Framework |
3 |
PIR |
Allen Human Reference Atlas - 3D |
1.0.0 |
RAS |
By convention, the coordinate system dimensions are the the following:
PIR (Posterior Inferior Right):
X
axis isAnterior-to-Posterior
Y
axis isSuperior-to-Inferior
Z
axis isLeft-to-Right
.
RAS (Right Anterior Superior):
X
axis isLeft-to-Right
Y
axis isPosterior-to-Anterior
Z
axis isInferior-to-Superior
Cell Locator
World space for 3D Views is in RAS (Right Anterior Superior) orientation where x axis = Left-to-Right
, y axis = Posterior-to-Anterior
and z axis = Inferior-to-Superior
.
CCF Atlas integration
Since the orientation header in the .nrrd
files used for the CCF are incorrect[1], Cell Locator workarounds the problem by applying two countermeasures: