Filters

These functions are tools for smoothing and filtering timeseries data.

pyneurotrace.filters.nndSmooth(data, hz, tau, iterFunc=None)

Performs fast non-negative temporal deconvolution for laser scanning microscopy.

Podgorski, K., & Haas, K. (2013). Fast non‐negative temporal deconvolution for laser scanning microscopy. Journal of biophotonics, 6(2), 153-162.

Parameters:

  • data (array) – Data array to be smoothed.

  • hz (int) – Sampling rate in Hz.

  • tau (float) – Time constant for the exponential decay.

  • iterFunc (function, optional) – Optional iteration function. Default is None.

Returns:

smoothed_data – Smoothed data array.

Return type:

array

pyneurotrace.filters.okada(data, iterFunc=None)

A computationally efficient filter for reducing shot noise in low S/N data.

Okada, M., Ishikawa, T., & Ikegaya, Y. (2016). A computationally efficient filter for reducing shot noise in low S/N data. PloS one, 11(6), e0157595.

Parameters:

  • data (array) – Data array to be filtered.

  • iterFunc (function, optional) – Optional iteration function. Default is None.

Returns:

filtered_data – Filtered data array.

Return type:

array

pyneurotrace.filters.deltaFOverF0(data, hz, t0=0.2, t1=0.75, t2=3.0, iterFunc=None)

Calculates the change in fluorescence over baseline fluorescence. Optionally smoothed with an EWMA.

Jia, H., Rochefort, N. L., Chen, X., & Konnerth, A. (2011). In vivo two-photon imaging of sensory-evoked dendritic calcium signals in cortical neurons. Nature protocols, 6(1), 28.

Parameters:

  • data (array) – Data array to be analyzed.

  • hz (int) – Sampling rate in Hz.

  • t0 (float, optional) – Time constant for exponential moving average. Default is 0.2.

  • t1 (float, optional) – Time window for calculating the mean baseline. Default is 0.75.

  • t2 (float, optional) – Time window for calculating the minimum baseline. Default is 3.0.

  • iterFunc (function, optional) – Optional iteration function. Default is None.

Returns:

deltaF_over_F0 – Calculated change in fluorescence over baseline fluorescence.

Return type:

array