baby.morph_thresh_seg.Group

class baby.morph_thresh_seg.Group(targets, min_area=10.0, use_thresh=False, thresh_expansion=0.0, pedge_thresh=None, interior_threshold=0.5, n_closing=0, n_opening=0, connectivity=2, edge_sub_dilations=None)

Bases: object

Attributes

interior_threshold

lower

max_n_erode

n_cells

n_erode

upper

Methods

segment(pred, border_rect[, fit_radial])

Obtain the cell masks, areas, edges, and coordiantes from the prediction of the interior of the cell group.

erode_predictions
prediction

__init__(targets, min_area=10.0, use_thresh=False, thresh_expansion=0.0, pedge_thresh=None, interior_threshold=0.5, n_closing=0, n_opening=0, connectivity=2, edge_sub_dilations=None)

Methods

__init__(targets[, min_area, use_thresh, ...])
erode_predictions(predictions)
prediction(pred, target_name[, erode])
segment(pred, border_rect[, fit_radial])	Obtain the cell masks, areas, edges, and coordiantes from the prediction of the interior of the cell group.

Attributes

interior_threshold
lower
max_n_erode
n_cells
n_erode
upper

segment(pred, border_rect, fit_radial=False)

Obtain the cell masks, areas, edges, and coordiantes from the prediction of the interior of the cell group.

Parameters

• fit_radial –

• pred – The neural network’s prediction

• border_rect – A boolean array delimiting the border of the prediction arrays