delta.pipeline.Position#
- class delta.pipeline.Position(position_nb, config)[source]#
Position-processing object.
- __init__(position_nb, config)[source]#
Initialize Position.
- Parameters
- position_nbint
Position index.
- configConfig
DeLTA configuration.
- Returns
- None.
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)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