API
===
Import livecellx as::

    import livecellx as lcx
    import livecellx
    import livecellx.annotation
    import livecellx.annotation.labelme2coco
    


Annotation
~~~~~~~~~~

.. module:: livecellx.annotation
.. currentmodule:: livecellx

.. autosummary::
    :toctree: api

    annotation.labelme2coco.get_coco_from_labelme_folder
    annotation.labelme2coco.convert

Classification
~~~~~~~~~~~~~~

.. module:: livecellx.classification
.. currentmodule:: livecellx

.. autosummary::
    :toctree: api

Core
~~~~

.. module:: livecellx.core
.. currentmodule:: livecellx

.. autosummary::
    :toctree: api

    core.datasets.read_img_default
    core.io_sc.process_scs_from_label_mask
    core.io_sc.process_mask_wrapper
    core.io_sc.prep_scs_from_mask_dataset
    core.io_utils.save_png
    core.io_utils.save_tiff
    core.io_utils.save_general
    core.pl_utils.add_colorbar
    core.sc_seg_operator.create_sc_seg_napari_ui
    core.sct_operator.create_sct_napari_ui
    core.sct_operator.create_scts_operator_viewer
    core.sct_operator.create_scs_edit_viewer

Model_zoo
~~~~~~~~~

.. module:: livecellx.model_zoo
.. currentmodule:: livecellx

.. autosummary::
    :toctree: api

Preprocess
~~~~~~~~~~

.. module:: livecellx.preprocess
.. currentmodule:: livecellx

.. autosummary::
    :toctree: api

Segment
~~~~~~~

.. module:: livecellx.segment
.. currentmodule:: livecellx

.. autosummary::
    :toctree: api

    segment.ou_simulator.viz_check_combined_sc_result
    segment.ou_simulator.compute_distance_by_contour
    segment.ou_simulator.combine_two_scs_monte_carlo
    segment.ou_simulator.gen_synthetic_overlap_scs
    segment.ou_simulator.gen_gauss_sc_bg
    segment.ou_simulator.gen_sc_bg_crop
    segment.ou_simulator.move_two_scs
    segment.utils.get_contours_from_pred_masks
    segment.utils.match_mask_labels_by_iou
    segment.utils.filter_labels_match_map
    segment.utils.compute_match_label_map
    segment.utils.process_scs_from_one_label_mask
    segment.utils.process_mask_wrapper
    segment.utils.prep_scs_from_mask_dataset
    segment.utils.judge_connected_bfs
    
Track
~~~~~

.. module:: livecellx.track
.. currentmodule:: livecellx

.. autosummary::
    :toctree: api

    track.classify_utils.video_frames_and_masks_from_sample
    track.classify_utils.combine_video_frames_and_masks
    track.sort_tracker.associate_detections_with_trackers

Trajectory
~~~~~~~~~~

.. module:: livecellx.trajectory
.. currentmodule:: livecellx

.. autosummary::
    :toctree: api

    trajectory.contour_utils.get_cellTool_contour_points
    trajectory.contour_utils.viz_contours
    trajectory.feature_extractors.compute_haralick_features
    trajectory.feature_extractors.compute_skimage_regionprops

Contour
~~~~~~~~

.. module:: livecellx.trajectory.contour
.. currentmodule:: livecellx

.. autosummary::
    :toctree: api