siibra.features.image.sections

Multimodal data features in 2D section.

Classes

BigBrain1MicronPatch	Base class for anatomically anchored data features.
CellbodyStainedSection	Base class for anatomically anchored data features.

Module Contents

class siibra.features.image.sections.BigBrain1MicronPatch(patch: siibra.locations.AxisAlignedPatch, profile: siibra.locations.Contour, section: CellbodyStainedSection, vertex: int, relevance: float, anchor: siibra.features.anchor.AnatomicalAnchor)

Base class for anatomically anchored data features.

__repr__()

fetch(flip: bool = False, resolution_mm: float = -1, **kwargs)

Fetch a volumetric or surface representation from one of the providers.

Parameters:

• format (str, default=None) –

  Requested format. If None, the first supported format matching in self.formats is tried, starting with volumetric formats. It can be explicitly specified as:

  • ’surface’ or ‘mesh’ to fetch a surface format

  • ’volumetric’ or ‘voxel’ to fetch a volumetric format

  • supported format types, see SUPPORTED_FORMATS. This includes

  ’nii’, ‘zip/nii’, ‘neuroglancer/precomputed’, ‘gii-mesh’, ‘neuroglancer/precompmesh’, ‘gii-label’

• **kwargs –

  • resolution_mm: resolution in millimeters as float or a tuple of floats

  • format: the format of the volume, like “mesh” or “nii”

  • voi: a BoundingBox of interest

Returns:

An image (Nifti1Image) or mesh (Dict[‘verts’

Return type:

ndarray, ‘faces’: ndarray, ‘labels’: ndarray])

get_boundingbox(**fetch_kwargs)

Enforce that the bounding box spans the full section thickness.

property bigbrain_section

property profile: siibra.locations.Contour

relevance

property section: CellbodyStainedSection

vertex

class siibra.features.image.sections.CellbodyStainedSection(**kwargs)

Base class for anatomically anchored data features.

get_boundingbox(clip=False, background=0, **fetch_kwargs)

Obtain the bounding box in physical coordinates of this volume.

Parameters:

• clip (bool, default: True) – Whether to clip the background of the volume.

• background (float, default: 0.0) – The background value to clip. .. note:: To use it, clip must be True.

• fetch_kwargs – key word arguments that are used for fetching volumes, such as voi or resolution_mm. Currently, only possible for Neuroglancer volumes except for format.

Raises:

RuntimeError – If the volume provider does not have a bounding box calculator.