neuralib.atlas.data
- neuralib.atlas.data.load_bg_structure_tree(atlas_name='allen_mouse_10um', check_latest=True, paired=False)[source]
Load structure dataframe or dict from brainglobe_atlasapi
- Parameters:
atlas_name (str) – allen source name
check_latest (bool) – if check the brainglobe api latest version
paired (bool) – To only
acronym&parent_acronymfields
- Returns:
- Return type:
DataFrame
- neuralib.atlas.data.get_children(parent: int, *, dataframe: bool = False, atlas_name: str = 'allen_mouse_10um') list[int] | DataFrame[source]
- neuralib.atlas.data.get_children(parent: str, *, dataframe: bool = False, atlas_name: str = 'allen_mouse_10um') list[str] | DataFrame
- neuralib.atlas.data.get_annotation_ids(atlas_name='allen_mouse_10um', check_latest=True)[source]
- Parameters:
atlas_name (str)
check_latest (bool)
- Return type:
ndarray
- neuralib.atlas.data.get_leaf_in_annotation(region, *, name=False, cached_file=None)[source]
Get a list of annotation {id, acronym} with given region {id, acronym}
- Parameters:
region (int | str) – region id or region acronym
name (bool) – If True, return acronym, otherwise return id
cached_file (str | Path | bytes | BinaryIO | BufferedIOBase | BufferedReader | None) – cached json for the annotation_leaf_map
- Returns:
List of annotation {id, acronym}
- Return type:
list[int] | list[str]
- neuralib.atlas.data.build_annotation_leaf_map(cached_file=None)[source]
Get all region id (key) and list of annotation id (values)
- Parameters:
cached_file (str | Path | bytes | BinaryIO | BufferedIOBase | BufferedReader | None) – cached json file
- Returns:
- Return type:
dict[int, list[int]]
- neuralib.atlas.data.get_dorsal_cortex(output_dir=None)[source]
Get example dorsal projection annotation svg file
- Parameters:
output_dir (Path | None) – Output directory for caching
- Returns:
Output file path
- Return type:
Path
- neuralib.atlas.data.load_allensdk_annotation(resolution=10, output_dir=None)[source]
DEPRECATED. Data Source directly from Allen Institute
See also
https://download.alleninstitute.org/informatics-archive/current-release/mouse_ccf/annotation/
- Parameters:
resolution (int) – volume resolution in um. default is 10 um
output_dir (str | Path | bytes | BinaryIO | BufferedIOBase | BufferedReader | None) – output directory for caching
- Returns:
Array[uint32, [AP, DV, ML]]
- Return type:
ndarray
- neuralib.atlas.data.load_ccf_annotation(output_dir=None)[source]
DEPRECATED.
- Parameters:
output_dir (str | Path | bytes | BinaryIO | BufferedIOBase | BufferedReader | None)
- Return type:
ndarray