New to Igor Pro - I need to clarify some doubts I have.

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Sun, 03/13/2011 - 04:48 am

Dear All,

I am new here (and new to Igor Pro) as well. I have just purchased the Igor Pro latest version (though I am waiting for the license key). I have never used this before - I have only been working with Axon Instruments / Clampex / Clampfit and ABF data files. But now, I have moved to a new lab, where they use HEKA Patchmaster for data acquisition. This is completely new to me as well.

I figured out that its not easy to export Patchmaster data files into Igor Binary files ( .itx) which can then be converted to ABF for analysis with Clampfit or MiniAnalysis (this was possible and fine with Pulse data files though). Anyway, so I have decided I might as well start using Igor Pro and learn how to use it.

So my questions / doubts:

(1) I have seen from the manuals and documentations that, th3 Patchmaster files can be analysed with Igor Pro - But first I need to export the patchmaster files into some Igor Pro format, isn't it? Or does Igor Pro automatically take in raw Patchmaster data files?

(2) I have seen that there is a tool called "Patchers Power Tools" that does this job - But I saw this information from SPACAN, which said to import the Patchmaster data files, first I need to export the data in Igor Binary Wave format and then these can be imported / analysed with Igor Pro / SPACAN. So, does this mean, this works only for data that needs to be analysed with SPACAN extension? Or does it apply to any data that needs to be imported into Igor Pro for analysis?

(3) I have also noticed "Data Access" for importing different file formats (including Patchmaster Raw Data files) into Igor Pro. Is this essential to buy (and it's quiet expensive)? Or is it just as fine to export the data files from Patchmaster in Igor Pro format and just go ahead with the analysis?

I apologize if the questions above are kind of silly or dumb - But as I had mentioned above, I have no idea about Igor Pro or Patchmaster.

Thanks a lot in advance. Cheers,
Sudhir
fonduekid wrote:
I figured out that its not easy to export Patchmaster data files into Igor Binary files ( .itx) which can then be converted to ABF for analysis with Clampfit or MiniAnalysis (this was possible and fine with Pulse data files though). Anyway, so I have decided I might as well start using Igor Pro and learn how to use it.

Right- ABF is a proprietary format that's quite complex, and Axon doesn't make it easy to deal with them.
Quote:
(1) I have seen from the manuals and documentations that, th3 Patchmaster files can be analysed with Igor Pro - But first I need to export the patchmaster files into some Igor Pro format, isn't it? Or does Igor Pro automatically take in raw Patchmaster data files?

Those .itx files are Igor Text File format. Just drop one on the Igor application and see what happens. Read about them by executing this command in Igor:
DisplayHelpTopic "Igor Text File Format"
Quote:
(2) I have seen that there is a tool called "Patchers Power Tools" that does this job - But I saw this information from SPACAN, which said to import the Patchmaster data files, first I need to export the data in Igor Binary Wave format and then these can be imported / analysed with Igor Pro / SPACAN. So, does this mean, this works only for data that needs to be analysed with SPACAN extension? Or does it apply to any data that needs to be imported into Igor Pro for analysis?

I think Patchmaster may have an option to export data as Igor binary wave format- that's a format that stores an Igor wave. But the .itx files should work fine as well. There may even be an option to export as an Igor .pxp file, if I remember correctly. That would be an Igor experiment file- the whole environment in Igor ready to go.
Quote:

(3) I have also noticed "Data Access" for importing different file formats (including Patchmaster Raw Data files) into Igor Pro. Is this essential to buy (and it's quiet expensive)? Or is it just as fine to export the data files from Patchmaster in Igor Pro format and just go ahead with the analysis?

No, you don't need Data Access, unless you have to use the raw data files. Either .itx or .ibw files can be loaded into Igor very easily because they are Igor formats.
Quote:

I apologize if the questions above are kind of silly or dumb - But as I had mentioned above, I have no idea about Igor Pro or Patchmaster.

I can't help with Patchmaster. But for Igor, if you haven't done it already, be sure to look at the Getting Started help, and go through at least the first half of the Guided Tours. Find Getting Started at the top of the Help menu.

Igor is a big, complicated, and somewhat idiosyncratic application. The Guided Tours will take you through some simple tasks that will introduce you to the way Igor "thinks".

John Weeks
WaveMetrics, Inc.
support@wavemetrics.com

March 14, 2011 at 10:35 am - Permalink


Thank you very much, John for the wonderful information and reply.

Yes, I have been seeing the Igor Pro Manual, the Video Tutorials, The getting started guide and everything. Slowly, I am beginning to get a feel for what it is about.

I did manage to load the Patchmaster files into Igor Pro (of course, after exporting them into igor pro format). Also, I have played around with the other tools like Patchers Power Tools and SPACAN.. PPT did load the Patchmaster files into Igor Pro and when I plot the wave, it plots out the particularly recording. I have not looked deeper into SPACAN for now, but I will in the future.

Meanwhile, there was one thing I failed to figure out in Igor Pro, after loading the Patchmaster Data files (I did this from Data > Load Waves > Load Igor Binary or Load Igor Text...)

How do I fix the region to be measured? I mean, lets say I want to measure the amplitude of an group of evoked responses. How do I fix the region in which the amplitude has to be measured? I was looking for something like a cursor or similar, that could be placed to define the region and then chose something from analysis. But I could not figure out how to do this. :(

Can you please let me know? Thanks in advance. (Of course, I am still going through in detail the manuals and tutorials.. I just thought I'll leave a note here if you can point me in the right direction) :)

PS., By the way, does anyone, who is working with whole cell patch clamp, have pre-defined macros or procedures, for measuring the amplitude of evoked responses, measuring the amplitude of currents induced by stimulation or uncaging, to plot the IV curves, and so on??

Thanks a lot.

Best,
Sudhir

March 15, 2011 at 03:12 am - Permalink

fonduekid wrote:
How do I fix the region to be measured? I mean, lets say I want to measure the amplitude of an group of evoked responses. How do I fix the region in which the amplitude has to be measured? I was looking for something like a cursor or similar, that could be placed to define the region and then chose something from analysis. But I could not figure out how to do this. :(

DisplayHelpTopic "Using Cursors"
That's part of the Guided Tour.
DisplayHelpTopic "Info Box and Cursors"
There are a few other places that talk about the graph cursors in the context of particular tasks.
Quote:
PS., By the way, does anyone, who is working with whole cell patch clamp, have pre-defined macros or procedures, for measuring the amplitude of evoked responses, measuring the amplitude of currents induced by stimulation or uncaging, to plot the IV curves, and so on??

You might want to look into Neuromatic at http://www.NeuroMatic.ThinkRandom.com/

John Weeks
WaveMetrics, Inc.
support@wavemetrics.com

March 15, 2011 at 11:00 am - Permalink

Thank you very much once again, John.

Yes, I am going through Neuromatic now. :) Thanks again.

March 15, 2011 at 12:21 pm - Permalink