allensdk.api.queries.reference_space_api module¶
- class allensdk.api.queries.reference_space_api.ReferenceSpaceApi(base_uri=None)[source]¶
Bases:
RmaApi
- ARA_NISSL = 'ara_nissl'¶
- AVERAGE_TEMPLATE = 'average_template'¶
- CCF_2015 = 'annotation/ccf_2015'¶
- CCF_2016 = 'annotation/ccf_2016'¶
- CCF_2017 = 'annotation/ccf_2017'¶
- CCF_VERSION_DEFAULT = 'annotation/ccf_2017'¶
- DEVMOUSE_2012 = 'annotation/devmouse_2012'¶
- MOUSE_2011 = 'annotation/mouse_2011'¶
- VOXEL_RESOLUTION_100_MICRONS = 100¶
- VOXEL_RESOLUTION_10_MICRONS = 10¶
- VOXEL_RESOLUTION_25_MICRONS = 25¶
- VOXEL_RESOLUTION_50_MICRONS = 50¶
- build_volumetric_data_download_url(data_path, file_name, voxel_resolution=None, release=None, coordinate_framework=None)[source]¶
Construct url to download 3D reference model in NRRD format.
- Parameters:
- data_pathstring
‘average_template’, ‘ara_nissl’, ‘annotation/ccf_{year}’, ‘annotation/mouse_2011’, or ‘annotation/devmouse_2012’
- voxel_resolutionint
10, 25, 50 or 100
- coordinate_frameworkstring
‘mouse_ccf’ (default) or ‘mouse_annotation’
Notes
See: 3-D Reference Models for additional documentation.
- download_annotation_volume(ccf_version, resolution, file_name)[source]¶
Download the annotation volume at a particular resolution.
- Parameters:
- ccf_version: string
Which reference space version to download. Defaults to “annotation/ccf_2017”
- resolution: int
Desired resolution to download in microns. Must be 10, 25, 50, or 100.
- file_name: string
Where to save the annotation volume.
- Note: the parameters must be used as positional parameters, not keywords
- download_mouse_atlas_volume(age, volume_type, file_name)[source]¶
Download a reference volume (annotation, grid annotation, atlas volume) from the mouse brain atlas project
- Parameters:
- agestr
Specify a mouse age for which to download the reference volume
- volume_typestr
Specify the type of volume to download
- file_namestr
Specify the path to the downloaded volume
- download_structure_mask(structure_id, ccf_version, resolution, file_name)[source]¶
Download an indicator mask for a specific structure.
- Parameters:
- structure_idint
Unique identifier for the annotated structure
- ccf_versionstring
Which reference space version to download. Defaults to “annotation/ccf_2017”
- resolutionint
Desired resolution to download in microns. Must be 10, 25, 50, or 100.
- file_namestring
Where to save the downloaded mask.
- download_structure_mesh(structure_id, ccf_version, file_name)[source]¶
Download a Wavefront obj file containing a triangulated 3d mesh built from an annotated structure.
- Parameters:
- structure_idint
Unique identifier for the annotated structure
- ccf_versionstring
Which reference space version to download. Defaults to “annotation/ccf_2017”
- file_namestring
Where to save the downloaded mask.
- download_template_volume(resolution, file_name)[source]¶
Download the registration template volume at a particular resolution.
- Parameters:
- resolution: int
Desired resolution to download in microns. Must be 10, 25, 50, or 100.
- file_name: string
Where to save the registration template volume.
- download_volumetric_data(data_path, file_name, voxel_resolution=None, save_file_path=None, release=None, coordinate_framework=None)[source]¶
Download 3D reference model in NRRD format.
- Parameters:
- data_pathstring
‘average_template’, ‘ara_nissl’, ‘annotation/ccf_{year}’, ‘annotation/mouse_2011’, or ‘annotation/devmouse_2012’
- file_namestring
server-side file name. ‘annotation_10.nrrd’ for example.
- voxel_resolutionint
10, 25, 50 or 100
- coordinate_frameworkstring
‘mouse_ccf’ (default) or ‘mouse_annotation’
Notes
See: 3-D Reference Models for additional documentation.