allensdk.api.queries.synchronization_api module

class allensdk.api.queries.synchronization_api.SynchronizationApi(base_uri=None)

Bases: allensdk.api.api.Api

HTTP client for image synchronization services uses the image alignment results from the Informatics Data Processing Pipeline. Note: all locations on SectionImages are reported in pixel coordinates and all locations in 3-D ReferenceSpaces are reported in microns.

See Image to Image Synchronization for additional documentation.

get_image_to_atlas(section_image_id, x, y, atlas_id)

For a specified Atlas, find the closest annotated SectionImage and (x,y) location as defined by a seed SectionImage and seed (x,y) location.

Parameters:

section_image_id : integer

Seed for spatial sync.

x : float

Pixel coordinate of the seed location in the seed SectionImage.

y : float

Pixel coordinate of the seed location in the seed SectionImage.

atlas_id : int

Target Atlas for image sync.

Returns:

dict

The parsed json response

get_image_to_image(section_image_id, x, y, section_data_set_ids)

For a list of target SectionDataSets, find the closest SectionImage and (x,y) location as defined by a seed SectionImage and seed (x,y) pixel location.

Parameters:

section_image_id : integer

Seed for spatial sync.

x : float

Pixel coordinate of the seed location in the seed SectionImage.

y : float

Pixel coordinate of the seed location in the seed SectionImage.

section_data_set_ids : list of integers

Target SectionDataSet IDs for image sync.

Returns:

dict

The parsed json response

get_image_to_image_2d(section_image_id, x, y, section_image_ids)

For a list of target SectionImages, find the closest (x,y) location as defined by a seed SectionImage and seed (x,y) location.

Parameters:

section_image_id : integer

Seed for image sync.

x : float

Pixel coordinate of the seed location in the seed SectionImage.

y : float

Pixel coordinate of the seed location in the seed SectionImage.

section_image_ids : list of ints

Target SectionImage IDs for image sync.

Returns:

dict

The parsed json response

get_image_to_reference(section_image_id, x, y)

For a specified SectionImage and (x,y) location, return the (x,y,z) location in the ReferenceSpace of the associated SectionDataSet.

Parameters:

section_image_id : integer

Seed for image sync.

x : float

Pixel coordinate on the specified SectionImage.

y : float

Pixel coordinate on the specified SectionImage.

Returns:

dict

The parsed json response

get_reference_to_image(reference_space_id, x, y, z, section_data_set_ids)

For a list of target SectionDataSets, find the closest SectionImage and (x,y) location as defined by a (x,y,z) location in a specified ReferenceSpace.

Parameters:

reference_space_id : integer

Seed for spatial sync.

x : float

Coordinate (in microns) of the seed location in the seed ReferenceSpace.

y : float

Coordinate (in microns) of the seed location in the seed ReferenceSpace.

z : float

Coordinate (in microns) of the seed location in the seed ReferenceSpace.

section_data_set_ids : list of ints

Target SectionDataSets IDs for image sync.

Returns:

dict

The parsed json response

get_structure_to_image(section_data_set_id, structure_ids)

For a list of target structures, find the closest SectionImage and (x,y) location as defined by the centroid of each Structure.

Parameters:

section_data_set_id : integer

primary key

structure_ids : list of integers

primary key

Returns:

dict

The parsed json response