Signal extraction¶

ImagingDataset.extract(rois=None, signal_channel=0, label=None, remove_overlap=True, n_processes=None, demix_channel=None)¶

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. If None, uses half the CPUs.
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.

Returns:

dict of arrays – Keys: raw, demixed_raw, mean_frame, overlap, signal_channel, rois, timestamp

Details¶

Methods used to extract signals from an ImagingDataset.