Signal extraction¶
- ImagingDataset.extract(rois=None, signal_channel=0, label=None, remove_overlap=True, n_processes=1, demix_channel=None, save_summary=True)¶
Extracts imaging data from the current dataset using the supplied ROIs file.
Parameters: - rois (sima.ROI.ROIList, optional) – ROIList of rois to extract
- signal_channel (string or int, optional) – Channel containing the signal to be extracted, either an integer index or a name in self.channel_names
- label (string or None, optional) – Text label to describe this extraction, if None defaults to a timestamp.
- remove_overlap (bool, optional) – If True, remove any pixels that overlap between masks.
- n_processes (int, optional) – Number of processes to farm out the extraction across. Should be at least 1 and at most one less then the number of CPUs in the computer. Defaults to 1.
- demix_channel (string or int, optional) – Channel to demix from the signal channel, either an integer index or a name in self.channel_names If None, do not demix signals.
- save_summary (bool, optional) – If True, additionally save a summary of the extracted ROIs.
Returns: Keys: raw, demixed_raw, mean_frame, overlap, signal_channel, rois, timestamp
Return type: dict of arrays
See also
Details¶
Methods used to extract signals from an ImagingDataset.