How to analyze spontaneous inhibitory post synaptic current (IPSC) in Clampfit?

Unlike my other articles, this is for people who are practising electrophysiologists. When I tried to find materials online on how to analyze the IPCSs that I have been recording from hippocampal neurons, I came up with very few sources most of which directed to MiniAnalysis software from synaptosoft. Personally, I was not a fan of this software due to its poor tutorial website. So I found a way to analyze these events in Clampfit (from Molecular devices). My primary aim was to find the averaged traces of all the events detected and measure different parameters like decay time constant and peak amplitude of the average trace. Given below are the steps:

Here is a sample of my raw data for reference:


Part I: Creating a template – This will be dragged across the recording to find matches.

create temp

  1. Click on Create Template under Event Detection Menu
  2. Bring cursors 1 and 2 on your best event trace
  3. Click Add
  4. Select another event trace that well represents your traces to be analyzed
  5. Click Add
  6. Click on Save As

Continue with steps 4 & 5 until satisfied. The program will take the average of all the added traces to find matches.

create temp2

Part II – Running the Template Search

  1. Click on Template Search under Event Detection menu
  2. The program will start highlighting individual event press “A” to Accept or “R” to reject events. Alternatively, Click on the “Non-Stop” (See screenshot below) icon in the event detection toolbar to accept all the events detected and then reject individually the events that do not qualify.
  3. Click on Save As in the event viewer window to save all the events detected which are aligned and superimposed. The default extension for saving is .abf if you need to save it in ASCII extension save it in .atf format. The event viewer should open automatically if not click on the event viewer icon in the toolbar (See screen shot).

detection toolbar event viewer

Some additional consideration of Template search is given in the graphics below:

Event Detection

After you have done all these you can open up the saved file with all your events and click on the average trace icon to get one single average trace of all the events displayed.



Leave a Reply

Fill in your details below or click an icon to log in: Logo

You are commenting using your account. Log Out /  Change )

Google+ photo

You are commenting using your Google+ account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )


Connecting to %s