ibllib.atlas.atlas

Classes for manipulating brain atlases, insertions, and coordinates.

Functions

AllenAtlas
BrainAtlas
BrainCoordinates
FranklinPaxinosAtlas
MRITorontoAtlas
NeedlesAtlas
deprecated_decorator

Classes

Insertion	Defines an ephys probe insertion in 3D coordinate.
Trajectory	3D Trajectory (usually for a linear probe), minimally defined by a vector and a point.

deprecated_decorator(function)

BrainCoordinates(*args, **kwargs)

BrainAtlas(*args, **kwargs)

class Trajectory(vector: ndarray, point: ndarray)

Bases: Trajectory

3D Trajectory (usually for a linear probe), minimally defined by a vector and a point.

Examples

Instantiate from a best fit from an n by 3 array containing xyz coordinates:

>>> trj = Trajectory.fit(xyz)

vector: ndarray

point: ndarray

class Insertion(x: float, y: float, z: float, phi: float, theta: float, depth: float, label: str = '', beta: float = 0)

Bases: Insertion

Defines an ephys probe insertion in 3D coordinate. IBL conventions.

To instantiate, use the static methods: Insertion.from_track and Insertion.from_dict.

x: float

y: float

z: float

phi: float

theta: float

depth: float

AllenAtlas(*args, **kwargs)

NeedlesAtlas(*args, **kwargs)

MRITorontoAtlas(*args, **kwargs)

FranklinPaxinosAtlas(*args, **kwargs)