Coordinate systems

The GUI reads and writes positions in the brain relative to bregma, while atlases and many registration tools use the Allen Common Coordinate Framework (CCF), whose origin is a corner of the atlas volume. This page explains the two and how they relate. The conversions themselves are in How to convert between CCF and IBL coordinates.

IBL coordinates

The traced trajectory (xyz_picks) and the channel locations (channel_locations) are given as x, y, z in µm, relative to bregma:

Axis	Direction	Positive towards
x	Medial–lateral (ML)	Right
y	Anterior–posterior (AP)	Anterior
z	Dorsal–ventral (DV)	Dorsal

Because z is positive dorsally and bregma sits on the skull surface, points inside the brain have negative z. For example, a point at [-2000, -3000, -2500] is 2 mm left of the midline, 3 mm posterior of bregma and 2.5 mm below it.

Internally the GUI works in metres; files use µm.

The Allen CCF

The Allen CCF is a 3D reference brain. Its coordinates are measured from the front, top, left corner of the atlas volume, with axes in the order anterior–posterior, dorsal–ventral, medial–lateral, each positive towards posterior, ventral and right. Tools that register histology to the Allen atlas usually give positions in this frame.

Bregma in the CCF

The two frames are related by the position of bregma in the CCF volume:

Axis	Bregma in the CCF
ML	5739 µm
AP	5400 µm
DV	332 µm

Converting between the frames means subtracting (or adding) this position, reordering the axes, and flipping the AP and DV directions. iblatlas does this with AllenAtlas.ccf2xyz and AllenAtlas.xyz2ccf. Every channel_locations file records the bregma position it was computed with, in its origin entry.

Atlas resolution

The GUI uses the 25 µm Allen atlas. Histology images given to the GUI must be registered to it, and region lookups are made at that resolution: features finer than 25 µm along the track cannot be resolved by the atlas regions.