allensdk.api.queries.mouse_connectivity_api module

class allensdk.api.queries.mouse_connectivity_api.MouseConnectivityApi(base_uri=None)

Bases: ReferenceSpaceApi, GridDataApi

HTTP Client for the Allen Mouse Brain Connectivity Atlas.

See: Mouse Connectivity API

PRODUCT_IDS = [5, 31]

build_reference_aligned_image_channel_volumes_url(data_set_id)

Construct url to download the red, green, and blue channels aligned to the 25um adult mouse brain reference space volume.

Parameters:

data_set_idintegerallensdk.api.queries

aka attachable_id

Notes

See: Reference-aligned Image Channel Volumes for additional documentation.

calculate_injection_centroid(injection_density, injection_fraction, resolution=25)

Compute the centroid of an injection site.

Parameters:

injection_density: np.ndarray

The injection density volume of an experiment

injection_fraction: np.ndarray

The injection fraction volume of an experiment

download_data_mask(path, experiment_id, resolution)

download_injection_density(path, experiment_id, resolution)

download_injection_fraction(path, experiment_id, resolution)

download_projection_density(path, experiment_id, resolution)

download_reference_aligned_image_channel_volumes(data_set_id, save_file_path=None)

Returns:

The well known file is downloaded

experiment_correlation_search(**kwargs)

Select a seed experiment and a domain over which the similarity comparison is to be made.

Parameters:

rowinteger

SectionDataSet.id to correlate against.

structureslist of integers or strings, optional

Integer Structure.id or String Structure.acronym.

hemispherestring, optional

Use ‘right’ or ‘left’. Defaults to both hemispheres.

transgenic_lineslist of integers or strings, optional

Integer TransgenicLine.id or String TransgenicLine.name. Specify ID 0 to exclude all TransgenicLines.

injection_structureslist of integers or strings, optional

Integer Structure.id or String Structure.acronym.

primary_structure_onlyboolean, optional

product_idslist of integers, optional

Integer Product.id

start_rowinteger, optional

For paging purposes. Defaults to 0.

num_rowsinteger, optional

For paging purposes. Defaults to 2000.

Notes

See Correlation Search and service::mouse_connectivity_correlation.

experiment_injection_coordinate_search(**kwargs)

User specifies a seed location within the 3D reference space. The service returns a rank list of experiments by distance of its injection site to the specified seed location.

Parameters:

seed_pointlist of floats

The coordinates of a point in 3-D SectionDataSet space.

transgenic_lineslist of integers or strings, optional

Integer TransgenicLine.id or String TransgenicLine.name. Specify ID 0 to exclude all TransgenicLines.

injection_structureslist of integers or strings, optional

Integer Structure.id or String Structure.acronym.

primary_structure_onlyboolean, optional

product_idslist of integers, optional

Integer Product.id

start_rowinteger, optional

For paging purposes. Defaults to 0.

num_rowsinteger, optional

For paging purposes. Defaults to 2000.

Notes

See Injection Coordinate Search and service::mouse_connectivity_injection_coordinate.

experiment_source_search(**kwargs)

Search over the whole projection signal statistics dataset to find experiments with specific projection profiles.

Parameters:

injection_structureslist of integers or strings

Integer Structure.id or String Structure.acronym.

target_domainlist of integers or strings, optional

Integer Structure.id or String Structure.acronym.

injection_hemispherestring, optional

‘right’ or ‘left’, Defaults to both hemispheres.

target_hemispherestring, optional

‘right’ or ‘left’, Defaults to both hemispheres.

transgenic_lineslist of integers or strings, optional

Integer TransgenicLine.id or String TransgenicLine.name. Specify ID 0 to exclude all TransgenicLines.

injection_domainlist of integers or strings, optional

Integer Structure.id or String Structure.acronym.

primary_structure_onlyboolean, optional

product_idslist of integers, optional

Integer Product.id

start_rowinteger, optional

For paging purposes. Defaults to 0.

num_rowsinteger, optional

For paging purposes. Defaults to 2000.

Notes

See Source Search, Target Search, and service::mouse_connectivity_injection_structure.

experiment_spatial_search(**kwargs)

Displays all SectionDataSets with projection signal density >= 0.1 at the seed point. This service also returns the path along the most dense pixels from the seed point to the center of each injection site..

Parameters:

seed_pointlist of floats

The coordinates of a point in 3-D SectionDataSet space.

transgenic_lineslist of integers or strings, optional

Integer TransgenicLine.id or String TransgenicLine.name. Specify ID 0 to exclude all TransgenicLines.

section_data_setslist of integers, optional

Ids to filter the results.

injection_structureslist of integers or strings, optional

Integer Structure.id or String Structure.acronym.

primary_structure_onlyboolean, optional

product_idslist of integers, optional

Integer Product.id

start_rowinteger, optional

For paging purposes. Defaults to 0.

num_rowsinteger, optional

For paging purposes. Defaults to 2000.

Notes

See Spatial Search and service::mouse_connectivity_target_spatial.

get_experiment_detail(experiment_id)

Retrieve the experiments data.

get_experiments(structure_ids, **kwargs)

Fetch experiment metadata from the Mouse Brain Connectivity Atlas.

Parameters:

structure_idsinteger or list, optional

injection structure

Returns:

urlstring

The constructed URL

get_experiments_api()

Fetch experiment metadata from the Mouse Brain Connectivity Atlas via the ApiConnectivity table.

Returns:

urlstring

The constructed URL

get_manual_injection_summary(experiment_id)

Retrieve manual injection summary.

get_projection_image_info(experiment_id, section_number)

Fetch meta-information of one projection image.

Parameters:

experiment_idinteger

section_numberinteger

Notes

See: image examples under Experimental Overview and Metadata for additional documentation. Download the image using allensdk.api.queries.image_download_api.ImageDownloadApi.download_section_image()

get_reference_aligned_image_channel_volumes_url(data_set_id)

Retrieve the download link for a specific data set. Notes —– See Reference-aligned Image Channel Volumes for additional documentation.

get_structure_unionizes(experiment_ids, is_injection=None, structure_name=None, structure_ids=None, hemisphere_ids=None, normalized_projection_volume_limit=None, include=None, debug=None, order=None)