fissa.deltaf module

Functions for computing correcting fluorescence signals for changes in baseline activity.

Authors:
  • Scott C Lowe
fissa.deltaf.findBaselineF0(rawF, fs, axis=0, keepdims=False)[source]

Find the baseline for a fluorescence imaging trace line.

The baseline, F0, is the 5th-percentile of the 1Hz lowpass filtered signal.

Parameters:
  • rawF (array_like) – Raw fluorescence signal.
  • fs (float) – Sampling frequency of rawF, in Hz.
  • axis (int, optional) – Dimension which contains the time series. Default is 0.
  • keepdims (bool, optional) – Whether to preserve the dimensionality of the input. Default is False.
Returns:

baselineF0 – The baseline fluorescence of each recording, as an array.
Return type:

numpy.ndarray

Note

In typical usage, the input rawF is expected to be sized (numROI, numTimePoints, numRecs) and the output will then be sized (numROI, 1, numRecs) if keepdims is True.