neuralib.atlas.view.SlicePlane

class neuralib.atlas.view.SlicePlane

Bases: object

2D Wrapper for a specific plane

__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

Methods

__init__(slice_index, ax, ay, dw, dh, slice_view)	Method generated by attrs for class SlicePlane.
plot([ax, to_um, annotation_region, ...])
plot_annotation_regions(ax, regions, extent)
plot_boundaries(ax, extent[, cmap, alpha])	Plot the annotation boundaries
with_angle_offset([deg_x, deg_y])	with degree offset
with_offset(dw, dh[, debug])

Attributes

slice_index	anchor index
ax	anchor x
ay	anchor y
dw	dw in um
dh	dh in um
slice_view	AbstractSliceView
unit
image
plane_offset
reference_value	relative to reference point

slice_index: int

anchor index

ax: int

anchor x

__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

ay: int

anchor y

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)

Parameters:

• dw (int)

• dh (int)

• debug (bool)

Return type:

Self

with_angle_offset(deg_x=0, deg_y=0)

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)

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 (str | list[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

plot_annotation_regions(ax, regions, extent, cmap='berlin', **kwargs)

plot_boundaries(ax, extent, cmap='binary', alpha=0.5, **kwargs)

Plot the annotation boundaries

Parameters:

• ax – Axes

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

• cmap – Colormap to be used for the annotation image. Defaults to ‘binary’.

• alpha – The imshow alpha, between 0 (transparent) and 1 (opaque). Defaults to 0.5.