Coordinate Systems


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



Allen Human Reference Atlas - 3D



By convention, the coordinate system dimensions are the the following:

  • PIR (Posterior Inferior Right):

    • X axis is Anterior-to-Posterior

    • Y axis is Superior-to-Inferior

    • Z axis is Left-to-Right.

  • RAS (Right Anterior Superior):

    • X axis is Left-to-Right

    • Y axis is Posterior-to-Anterior

    • Z axis is Inferior-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:

  1. It associates a RAStoPIR transform[2] with both the loaded CCF average template and annotation volumes..

  2. It updates the slice orientation preset associated with the coronal viewer[3] so that +x is +P.