neuralib.atlas.view.SlicePlane

class neuralib.atlas.view.SlicePlane[source]

Bases: object

2D Wrapper for a specific plane

slice_index: int

anchor index

ax: int

anchor x

ay: int

anchor y

__init__(slice_index, ax, ay, dw, dh, slice_view, unit='a.u.')

Method generated by attrs for class SlicePlane.

Parameters:

  • slice_index (int)

  • ax (int)

  • ay (int)

  • dw (int)

  • dh (int)

  • slice_view (AbstractSliceView)

  • unit (str)

Return type:

None

dw: int

dw in um

dh: int

dh in um

slice_view: AbstractSliceView

AbstractSliceView

unit: str
property image: ndarray
property plane_offset: ndarray
property reference_value: float

relative to reference point

with_offset(dw, dh, debug=False)[source]
Parameters:

  • dw (int)

  • dh (int)

  • debug (bool)

Return type:

Self

with_angle_offset(deg_x=0, deg_y=0)[source]

with degree offset

Parameters:

  • deg_x (float) – degree in x axis (width)

  • deg_y (float) – degree in y axis (height)

Returns:

Return type:

Self

plot(ax=None, to_um=True, annotation_region=None, boundaries=False, with_title=False, extent=None, reference_bg_value=None, annotation_cmap='berlin', annotation_rescale=True, **kwargs)[source]
Parameters:

  • ax (Axes | None) – The Axes object on which to plot. If None, a new figure and axes are created.

  • to_um (bool) – A boolean flag indicating whether the coordinates should be converted to micrometers. Defaults to True. Only applicable if extent is None.

  • annotation_region (list[str] | str | None) – The annotation region on which to plot. Defaults to None.

  • boundaries (bool) – A boolean indicating whether to include annotations in the plot.

  • with_title (bool) – A boolean indicating whether to include a title in the plot.

  • extent (tuple[float, float, float, float] | None) – A tuple defining the image boundaries (left, right, bottom, top). If None, boundaries are computed internally.

  • reference_bg_value (float | None) – If specified, remove background of its value in when view_type is reference (i.e., set as 10).

  • annotation_cmap (str) – Cmap for the annotation regions if specified

  • annotation_rescale (bool) – Rescale the image when view_type is annotation.

  • kwargs – Additional keyword arguments passed to ax.imshow().

Return type:

None