TT-scna

Summary

This package will perform single-channel noise analysis on an electrophysiological trace containing whole-cell currents recorded during the presence or absence of an activating stimulus.

Originally designed for use on whole-cell currents from HEK cells expressing channel rhodopsins, and being exposed to 'light' and 'dark' conditions. Please see the literature below for a (1) paper which inspired this work, and (2) an excellent review on single-channel noise analysis.

1. Govorunova, Elena G., et al. "Characterization of a highly efficient blue-shifted channelrhodopsin from the marine alga Platymonas subcordiformis." Journal of Biological Chemistry 288.41 (2013): 29911-29922.
2. Gray, PETER TA. "Analysis of whole cell currents to estimate the kinetics and amplitude of underlying unitary events: relaxation and ‘noise’analysis." Microelectrodes Techniques, The Plymouth Workshop Handbook. Second edition. D. Ogden, editor. Company of Biologists, Cambridge, MA. 1994.

Usage:

pip install ttscna
from ttscna import ttscna
ttscna.ttscna(file_name, on_start, off_start, sweep_len = 5.0, sample_rate = 20000, skip_rows = 9, sep = "\t", fmin = 20.0, fmax = 10000.0)

Doc-String

Takes as input a text file containing electrophysiological data in two conditions. Computes the difference in single-channel noise between the two conditions.

Must contain one column, with time, expressed in seconds, and a second column, with current, expressed in picoamps.

Inputs

file_name: str Path and File_name to text data file.

on_start: float Start time of 'on' condition.

off_start: float Start time of 'off' condition.

sweep_len: float Length of time, in seconds, of each condition to analyze.

sample_rate: float Sampling rate of the time series, in Hz.

skip_rows: int Rows to skip in the header of the data file.

sep: str Delimiter used in each column for the data file.

fmin: float Minimum frequency to fit to, in Hz.

fmax: float Maximum frequency to fit to, in Hz.

Output

Figure: .png A 4-panel plot containing:

100 microsecond traces of the On and Off conditions.

Overlaid power spectra from both conditions.
    
The power spectra of the on condition minus the off condition, 
overlaid with a Lorentzian model.

Table: .csv A .csv containing:

Unitary conductance, in fS.

Mean Dwell Time, in ms.
    
Mean Bulk Current, in pA.