neuralib.imaging.fov.ObjectiveFov

class neuralib.imaging.fov.ObjectiveFov

Bases: object

Class for 2P Field Of View coordinates

Use IBL coordinates space

AP (+), anterior to the Bregma. (-) posterior to the Bregma

ML (+), right hemisphere. (-) left hemisphere

See also

https://int-brain-lab.github.io/iblenv/notebooks_external/atlas_working_with_ibllib_atlas.html#Coordinate-systems

__init__(region_name, am, pm, al, pl, *, rotation_angle_ml=0, rotation_angle_ap=0, unit='mm')

Method generated by attrs for class ObjectiveFov.

Parameters:

• region_name (str)

• am (ndarray)

• pm (ndarray)

• al (ndarray)

• pl (ndarray)

• rotation_angle_ml (float)

• rotation_angle_ap (float)

• unit (Literal['mm', 'um'])

Return type:

None

Methods

__init__(region_name, am, pm, al, pl, *[, ...])	Method generated by attrs for class ObjectiveFov.
ap_invert()	anterior posterior coordinates invert
invert_axis()	invert both ap and ml axes
ml_invert()	medial lateral coordinates invert
to_polygon(**kwargs)	coordinates to matplotlib.patches.Polygon
to_um()	unit from mm to um

Attributes

region_name	FOV name
am	anteromedial (default in mm).
pm	posteromedial (default in mm).
al	anterolateral (default in mm).
pl	posterolateral (default in mm).
rotation_angle_ml	objective ml direction rotation in deg
rotation_angle_ap	objective ap direction rotation in deg
unit
ap_distance	anterior to posterior distance of the FOV
ml_distance	medial to lateral distance of the FOV

region_name: str

FOV name

am: ndarray

anteromedial (default in mm). Array[float, 2] in XY

pm: ndarray

posteromedial (default in mm). Array[float, 2] in XY

al: ndarray

anterolateral (default in mm). Array[float, 2] in XY

pl: ndarray

posterolateral (default in mm). Array[float, 2] in XY

rotation_angle_ml: float

objective ml direction rotation in deg

rotation_angle_ap: float

objective ap direction rotation in deg

unit: Literal['mm', 'um']

__init__(region_name, am, pm, al, pl, *, rotation_angle_ml=0, rotation_angle_ap=0, unit='mm')

Method generated by attrs for class ObjectiveFov.

Parameters:

• region_name (str)

• am (ndarray)

• pm (ndarray)

• al (ndarray)

• pl (ndarray)

• rotation_angle_ml (float)

• rotation_angle_ap (float)

• unit (Literal['mm', 'um'])

Return type:

None

property ap_distance: float

anterior to posterior distance of the FOV

property ml_distance: float

medial to lateral distance of the FOV

to_um()

unit from mm to um

Return type:

Self

ap_invert()

anterior posterior coordinates invert

Return type:

Self

ml_invert()

medial lateral coordinates invert

Return type:

Self

invert_axis()

invert both ap and ml axes

Return type:

Self

to_polygon(**kwargs)

coordinates to matplotlib.patches.Polygon

Return type:

Polygon