"""
Module containing main pipeline for user mode as well as calls for pipeline functions.
"""

from ._preprocess import reorder_shape
from ._preprocess import reorder_image_stack
from ._preprocess import prepare_image_detection
from ._preprocess import convert_parameters_types

from .segmentation import launch_segmentation
from .segmentation import _cast_segmentation_parameters
from .segmentation import cell_segmentation
from .segmentation import plot_segmentation

from .detection import launch_detection
from .detection import launch_features_computation
from .detection import launch_cell_extraction
from .detection import get_nucleus_signal
from .detection import output_spot_tiffvisual

from .spots import launch_spots_extraction