delta.pipeline.Position

class delta.pipeline.Position(position_nb, config)

Position-processing object.

__init__(position_nb, config)

Initialize Position.

Parameters:

position_nbint

Position index.

configConfig

DeLTA configuration.

Methods

__init__(position_nb, config)	Initialize Position.
clear()	Clear Position-specific variables from memory (can be loaded back with load()).
compare(other[, level])	Compare this Position with another and print the differences.
compute_growthrates(frames[, smooth_frames])	Extract features for all ROIs in frames.
find_roi_boxes(reference, config[, ...])	Use U-Net to detect ROIs (chambers etc...).
labels([frames, undo_corrections])	Generate full-size frames with labelled cells.
load_netcdf(filename)	Load position from netCDF file.
preprocess(all_frames, frames[, reference])	Pre-process position (Rotation correction, identify ROIs, initialize drift correction).
results_movie(reader[, frames, with_labels])	Generate movie illustrating segmentation and tracking.
save([filename, frames, reader, save_as, ...])	Save to disk.
segment(frames, *[, progress_bar])	Segment cells in all ROIs in position.
to_netcdf(path, *[, progress_bar])	Save the position as a netCDF file.
track(frames, *[, progress_bar])	Track cells in all ROIs in position.

Attributes

position_nb	Position index number in the experiment
shape	Shape of full-frame images.
rois	List of ROI objects under position
drift_values	XY drift correction values over time
rotate	Rotation angle of the position to compensate
config	Configuration parameters object