colocalization

class ColocalizationProcessor(sample_manager: SampleManager | None = None, config_coordinator: ConfigCoordinator | None = None, channels: List[str] | None = None, registration_processor: RegistrationProcessor | None = None)

Bases: CompoundChannelPipelineOrchestrator

compute_colocalization(channel_a, channel_b)

filter_table(channel_a, channel_b)

finalise_setup()

get_cells_df(channel)

get_voxelization_params(channel_a, channel_b)

plot_nearest_neighbors(channel_a, channel_b, parent=None)

plot_overlaps()

save_filtered_table(channel_a, channel_b)

setup(sample_manager: SampleManager | None, channel_names: tuple[str], registration_processor: RegistrationProcessor | None = None)

Attach a sample manager and mark this processor as ready.

Parameters:

sample_manager (SampleManager, optional) – If provided, replaces the currently stored sample manager. When None, the previously stored instance is reused.

Raises:

ValueError – If the config section identified by config_name is absent.

voxelize_filtered_table(channel_a, channel_b)

voxelize_unweighted(channel_a, channel_b, coordinates, voxelization_parameter)

Voxelize un weighted i.e. for cell counts

Parameters:

• channel_a (str) – Name of the first channel

• channel_b (str) – Name of the second channel

• coordinates (str, array or Source) – Source of point of nxd coordinates.

• voxelization_parameter (dict) –

  Dictionary to be passed to voxelization.voxelise (i.e. with these optional keys:

  shape, dtype, weights, method, radius, kernel, processes, verbose

Returns

coordinates, counts_file_path: np.array, str

colocalization_channels: dict[Channel]

config_name = 'colocalization'