siibra.features.image

Multimodal data features in volume or image formats.

Submodules

Classes

`BigBrain1MicronPatch`	Base class for anatomically anchored data features.
`BlockfaceVolumeOfInterest`	Base class for anatomically anchored data features.
`CellBodyStainedVolumeOfInterest`	Base class for anatomically anchored data features.
`CellbodyStainedSection`	Base class for anatomically anchored data features.
`DTIVolumeOfInterest`	Base class for anatomically anchored data features.
`LSFMVolumeOfInterest`	Base class for anatomically anchored data features.
`MRIVolumeOfInterest`	Base class for anatomically anchored data features.
`MorphometryVolumeOfInterest`	Base class for anatomically anchored data features.
`PLIVolumeOfInterest`	Base class for anatomically anchored data features.
`XPCTVolumeOfInterest`	Base class for anatomically anchored data features.

Package Contents

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

Inheritance diagram of siibra.features.image.BigBrain1MicronPatch

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’

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.BlockfaceVolumeOfInterest(**kwargs): Base class for anatomically anchored data features.

class siibra.features.image.CellBodyStainedVolumeOfInterest(**kwargs): Base class for anatomically anchored data features.

class siibra.features.image.CellbodyStainedSection(**kwargs): Base class for anatomically anchored data features.

class siibra.features.image.DTIVolumeOfInterest(modality, **kwargs): Base class for anatomically anchored data features.

class siibra.features.image.LSFMVolumeOfInterest(modality, **kwargs): Base class for anatomically anchored data features.

class siibra.features.image.MRIVolumeOfInterest(modality, **kwargs): Base class for anatomically anchored data features.

class siibra.features.image.MorphometryVolumeOfInterest(modality, **kwargs): Base class for anatomically anchored data features.

class siibra.features.image.PLIVolumeOfInterest(modality, **kwargs): Base class for anatomically anchored data features.

class siibra.features.image.XPCTVolumeOfInterest(modality, **kwargs): Base class for anatomically anchored data features.