allensdk.api.queries.reference_space_api module

class allensdk.api.queries.reference_space_api.ReferenceSpaceApi(base_uri=None)

Bases: allensdk.api.queries.rma_api.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)

Construct url to download 3D reference model in NRRD format.

Parameters:

data_path : string

‘average_template’, ‘ara_nissl’, ‘annotation/ccf_{year}’, ‘annotation/mouse_2011’, or ‘annotation/devmouse_2012’

voxel_resolution : int

10, 25, 50 or 100

coordinate_framework : string

‘mouse_ccf’ (default) or ‘mouse_annotation’

Notes

See: 3-D Reference Models for additional documentation.

download_annotation_volume(**kwargs)

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(**kwargs)

Download a reference volume (annotation, grid annotation, atlas volume) from the mouse brain atlas project

Parameters:

age : str

Specify a mouse age for which to download the reference volume

volume_type : str

Specify the type of volume to download

file_name : str

Specify the path to the downloaded volume

download_structure_mask(**kwargs)

Download an indicator mask for a specific structure.

Parameters:

structure_id : int

Unique identifier for the annotated structure

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 downloaded mask.

download_structure_mesh(**kwargs)

Download a Wavefront obj file containing a triangulated 3d mesh built from an annotated structure.

Parameters:

structure_id : int

Unique identifier for the annotated structure

ccf_version : string

Which reference space version to download. Defaults to “annotation/ccf_2017”

file_name : string

Where to save the downloaded mask.

download_template_volume(**kwargs)

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)

Download 3D reference model in NRRD format.

Parameters:

data_path : string

‘average_template’, ‘ara_nissl’, ‘annotation/ccf_{year}’, ‘annotation/mouse_2011’, or ‘annotation/devmouse_2012’

file_name : string

server-side file name. ‘annotation_10.nrrd’ for example.

voxel_resolution : int

10, 25, 50 or 100

coordinate_framework : string

‘mouse_ccf’ (default) or ‘mouse_annotation’

Notes

See: 3-D Reference Models for additional documentation.