I have recorded data using both current clamp and voltage clamp.
For Current Clamp, I found it very easy and straight forward to analyze action potentials and frequency in Spike 2; however, I find it extremely difficult to discern EPSCs from noise and artifact due to the varying amplitudes in Spike. Also, with the application of my peptide, the Vm/current often changes so the baseline is offset (so setting up a protocol to determine peaks below -X usually results in every data point after application being assessed as a peak).
Does anyone have any suggestions for script or different program?
Other possibilities (not free though) are:
- Igor Pro (this is my software of choice - from Wavemetrics): use it with the Neuromatic extension (free for download) or write your own code. If you know coding, it looks very similar to C. If you don't, there is a learning curve before writing it though.
-Mini Analysis (Synaptosoft): very commonly used program for this type of analysis. It has a built-in feature for importing ABF files.
Good luck with your analysis!
Andre
Hi Mary,
As it was already mentioned, one option would be to go with MiniAnalysis from Synaptosoft (http://www.synaptosoft.com/MiniAnalysis/index.html). Yet, I am not sure if they are still active and you can buy it.
Another option is to go with ClampFit which is a part of Axon's PClamp software package for the analysis. By using ClampFit you can create a template based on EPSCs events that you recorded and run that template in manual or auto mode (first is always better). And you don't have to worry about the changes in the baseline offset (if it is not something robust, of course).
Also you can go with setting several thresholds (this option is better for neuronal firing as to me).
The critical point is that ClampFit works with ABF files, so you may need to look for a converter if Spike files are not of abf. format.
Off-notes on "I find it extremely difficult to discern EPSCs from noise and artifact" - the best would be to count only events that are 2.5-3x more in amplitude than the amplitude of noise (amplitude of the baseline without events). So if noise of your trace is 3 pA it would be better to count those EPSCs which amplitudes are higher than 7.5 pA. One can easily set such a threshold (cut-off) in MiniAnalysis, Clampfit or WinEDR for sure.
Best,
Miroslav
Hi Mary, Easy Electrophysiology (www.easyelectrophysiology.com) is a software for the analysis of patch-clamp data, including EPSC analysis. There are many thresholding options which include a curved (polynomial) fit to the data that should work well for the case you described.
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