neuralib.imaging.cellular.CellularCoordinates

final class neuralib.imaging.cellular.CellularCoordinates

Bases: object

Container with coordinates information (in mm) for each ROIs

Dimension parameters:

N: number of neurons

P: number of plane types

__init__(neuron_idx, ap, ml, *, plane_index=None, source_plane_index=None, value=None, unit='mm')

Method generated by attrs for class CellularCoordinates.

Parameters:

• neuron_idx (ndarray)

• ap (ndarray)

• ml (ndarray)

• plane_index (int | ndarray | None)

• source_plane_index (ndarray | None)

• value (ndarray | None)

• unit (Literal['mm', 'um'])

Return type:

None

Methods

__init__(neuron_idx, ap, ml, *[, ...])	Method generated by attrs for class CellularCoordinates.
ap_rotate()
check(attribute, value)
in_relative_bregma(fov)	TODO check register cellular coordinates to IBL coordinates space
ml_rotate(x, y, deg)	calculate the values for x axis rotation
to_um()	unit from mm to um
with_selection(mask)	masking for cell selection
with_value(value)	assign value for CellularCoordinates

Attributes

neuron_idx	neuron index.
ap	anterior posterior coordinates (default in mm).
ml	medial lateral coordinates (default in mm).
plane_index	optic plane index.
source_plane_index	neuron's corresponding image plane.
value	metric (i.e., used in topographical analysis).
unit	unit of the coordinates.

neuron_idx: ndarray

neuron index. Array[float, N]

ap: ndarray

anterior posterior coordinates (default in mm). Array[float, N]

ml: ndarray

medial lateral coordinates (default in mm). Array[float, N]

plane_index: int | ndarray | None

optic plane index. i.e., used for depth analysis. If array type, Array[int, P]

source_plane_index: ndarray | None

neuron’s corresponding image plane. Array[float, N]

value: ndarray | None

metric (i.e., used in topographical analysis). Array[float, N]

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

unit of the coordinates. {‘mm’, ‘um’}

__init__(neuron_idx, ap, ml, *, plane_index=None, source_plane_index=None, value=None, unit='mm')

Method generated by attrs for class CellularCoordinates.

Parameters:

• neuron_idx (ndarray)

• ap (ndarray)

• ml (ndarray)

• plane_index (int | ndarray | None)

• source_plane_index (ndarray | None)

• value (ndarray | None)

• unit (Literal['mm', 'um'])

Return type:

None

check(attribute, value)

to_um()

unit from mm to um

Return type:

Self

with_value(value)

assign value for CellularCoordinates

Parameters:

value (ndarray) – value array for the corresponding coordinates. Array[float, N]

Returns:

Return type:

Self

with_selection(mask)

masking for cell selection

Parameters:

mask (ndarray) – numpy bool array. Array[bool, N]

Return type:

Self

in_relative_bregma(fov)

TODO check register cellular coordinates to IBL coordinates space

Parameters:

fov (ObjectiveFov) – ObjectiveFov

Return type:

Self

static ml_rotate(x, y, deg)

calculate the values for x axis rotation

Parameters:

• x (ndarray) – coordinate x. Array[float, N]

• y (ndarray) – coordinate Y. Array[float, N]

• deg (float) – rotation degree

Returns:

value to be subtracted. dx (N,) and dy (N,)

Return type:

tuple[ndarray, ndarray]

static ap_rotate()