delta.pipeline.Pipeline.preprocess

Pipeline.preprocess(positions: Optional[List[int]] = None, references: Optional[ndarray] = None, ROIs: Optional[str] = 'model')

Pre-process positions (Rotation correction, identify ROIs, initialize drift correction)

Parameters

positionslist of int or None, optional

List of positions to pre-process. If None, all will be run. The default is None.

references3D array or None, optional

Reference images to use to perform pre-processing. If None, the first image of each position will be used. Dimensions are (positions, size_y, size_x) The default is None.

ROIsNone or ‘model’, optional

Regions of interest. If None, whole frames are treated as one ROI. If ‘model’, the ROIs model from cfg.model_file_rois will be used to detect them. Otherwise, a list of ROIs can be provided in the format of the utilities.py cropbox function input box. The default is ‘model’.

Returns

None.