livecellx.core.sc_seg_operator.ScSegOperator

class livecellx.core.sc_seg_operator.ScSegOperator(sc, viewer, shape_layer=None, face_color=(0, 0, 1, 1), magicgui_container=None, csn_model=None, create_sc_layer=True, sct_observers=None)[source]

A class for performing segmentation on single cell images.

viewer

The napari viewer.

Type: napari.Viewer

sc

The single cell static object.

Type: SingleCellStatic

shape_layer

The napari shape layer for displaying the segmentation.

Type: napari.layers.Shapes

Parameters

viewer (napari.Viewer) – The napari viewer.
sc (SingleCellStatic) – The single cell static object.

Methods

`clear_sc_layer_callback`()
`close`()
`correct_segment`(model[, create_ou_input_kwargs])
`create_sc_layer`([name, contour_sample_num])
`csn_correct_seg_callback`([padding_pixels, ...])
`filter_cells_by_size_callback`(min_size, max_size)
`filter_contours_by_size`(contours, min_size, ...)
`focus_on_sc_callback`()
`hide_function_widgets`()
`load_default_csn_model`(path[, cuda])
`notify_sct_to_remove_sc_operator`()
`notify_sct_to_update`()
`remove_sc_layer`()
`replace_sc_contour`(contour[, ...])
`resample_contour`(contour[, sample_num, ...])
`resample_contours_callback`(sample_num)
`restore_sc_contour_callback`()
`save_seg_callback`()	Save the segmentation to the single cell object.
`setup_edit_contour_shape_layer`()
`show_selected_mode_widget`()
`update_shape_layer_by_sc`([contour_sample_num])

Attributes

`CSN_CORRECT_SEG_MODE`
`DEFAULT_CSN_MODEL`
`MANUAL_CORRECT_SEG_MODE`