Beta Module

Beta functions

exm.beta.beta.algin_channels(args, code_fov_pairs, parallel_processes=1)

Applies alignment between other channels and DAPI within the same round and fov.

Parameters:

• args (Args)

• parallel_processes (int)

Return type:

None

exm.beta.beta.algin_channels_function(args, tasks_queue, q_lock)

Applies alignment between other channels and DAPI within the same round and fov.

exm.beta.beta.algin_channels_function_new(args, tasks_queue, q_lock)

Applies alignment between other channels and DAPI within the same round and fov.

exm.beta.beta.algin_channels_new(args, code_fov_pairs, parallel_processes=1)

Applies alignment between other channels and DAPI within the same round and fov.

Parameters:

• args (Args)

• parallel_processes (int)

Return type:

None

exm.beta.beta.blend_ind(offsets, pictures, indices=None, inverts=None)

Blends a list of volume tiles together according to specified offsets, accounting for different z-stack sizes and starting points.

Parameters:

• offsets (ndarray) – An array of offsets for each image tile.

• pictures (List[ndarray]) – A list of image tiles to blend.

• indices (List[int] | None) – Optional list of indices specifying the order in which to blend the images.

• inverts (List[int] | None) – Optional list of axes along which to invert the corresponding image tiles.

Returns:

The blended image.

Return type:

ndarray

exm.beta.beta.foreground_segmentation(args)

Applies forground_segmentation on code 0 DAPI for each fov.

exm.beta.beta.foreground_segmentation_new(args)

Applies forground_segmentation on code 0 DAPI for each fov.

exm.beta.beta.quantile_normalization(args, code, fov)

Applies quantile normalization to the volumes aligned .h5 file.

Parameters:

• args (Args) – Configuration options. This should be an instance of the Args class.

• code (int) – The code of the volume to be normalized.

• fov (int) – The field of view of the volume to be normalized.

Return type:

None