amikroulis / simplified-test-pulse-analysis

Analysis tool for basic voltage-clamp parameters.

If you are running this for the first time, run the check packages.py first, to check if any packages are missing.

The analysis.py will open the main script to process the HEKA/abf files.

Requirements
Needs the voltage command trace as well as the current trace to be saved in the files.
For ABF files:
A folder with .abf files.

For HEKA files:
A folder with .dat files, and their corresponding .inf files (you get the .inf file from PatchMaster Replay menu)

A negative-going test pulse in voltage-clamp and at a sampling rate of at least 10 kHz is expected. If your protocol is different, you can change the fitting parameters in the tp.py file. Reaching the steady-state by the end of the pulse is essential for the analysis.
The test pulse results include the following, for the median sweep and for individual sweeps:
- estimated resting membrane potential (RMP)
- estimated input resistance including the series resistance (Rin)
- estimated series resistance (Rs)
- estimated capacitance (Cm)

For the inward/outward currents, the following are calculated for every voltage step:
- positive peak amplitude
- negative peak amplitude
- baseline current (steady-state)
- Na current estimate
- fast K current estimate
- slow K current estimate

Operation

0. select the file type (HEKA/Axon)
1. click Scan
2. select the folder with the recordings
3. switch to the 2nd tab (test pulse)
4. select the protocol name for the test pulse and the channel for the current trace
5. check the box for TP on the top right
6. add a log note or custom name for the results folder if needed (boxes on the right side)
7. click run and confirm the folder with the data files
8. wait (it will say “finished” when it’s done).

Results are placed in the same folder with the recordings, as: a HTML overview file, a CSV file with the tabulated results, a folder with results and intermediate processing step files for each recording.

Copyright 2018-2022 Apostolos Mikroulis, Eliška Waloschková.

This software is provided under terms of the zlib license.