The Nanoscale World

Extraction of peakforce Capture data with Matlab

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pfreumo posted on Wed, Jan 9 2013 9:37 AM

Hi there,

I'm trying to load data of a .pfc file into Matlab. I'm working with  Mac OSX. I tried the NSMatlabExamples.m file from the lates Analysis folder after copying the NSMatlabUtilities method into my Matlab folder, too.

When I use  filename = strcat( path/filename.psc) and run the method NSMatlabExamples it asks for a DataSourceDLL.h file. I think DLL files are windows based so I dont know how to proceed.

 

Any help is appreciated,

 

Best 

Moritz

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Verified by pfreumo

Hi Moritz,

As you noticed, the NSMatlabExamples program relys on DLLs that are installed with Nanoscope Analysis.  Nanoscope Analysis and the DLLs are only available for windows, so you will not be able to use that method if you must stick with your Mac. 

It is still possible to read the binary PFC file from Matlab, but you will have to parse the header and figure out the size and offset of the binary data on your own.  I would suggest searching this forum for 'Matlab'.  You will find some discussions like this one: http://nanoscaleworld.bruker-axs.com/nanoscaleworld/forums/p/853/2106.aspx#2106 that cover other Nanoscope data types (but I didn't see any for PFC or force volume).  The Nanoscope manual also has information about file formats -- see Appendix A.

--Bede

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Top 10 Contributor
280 Posts
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Bruker Employee
Verified by pfreumo

Hi Moritz,

As you noticed, the NSMatlabExamples program relys on DLLs that are installed with Nanoscope Analysis.  Nanoscope Analysis and the DLLs are only available for windows, so you will not be able to use that method if you must stick with your Mac. 

It is still possible to read the binary PFC file from Matlab, but you will have to parse the header and figure out the size and offset of the binary data on your own.  I would suggest searching this forum for 'Matlab'.  You will find some discussions like this one: http://nanoscaleworld.bruker-axs.com/nanoscaleworld/forums/p/853/2106.aspx#2106 that cover other Nanoscope data types (but I didn't see any for PFC or force volume).  The Nanoscope manual also has information about file formats -- see Appendix A.

--Bede

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Top 500 Contributor
3 Posts
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Hi!

 

So... Is there any way to load forces from PeakForce capture file *.pfc into Matlab using Windows?

The only functions in Nanoscope Analysis 64bit 1.50 build r2.103555 which gets nonzero data is related with force volume. For example, NSMU.CreateForceVolumeForceCurveZplot gets some data but not correct!

Even NSMU.GetRampSize returns zero!

 

Why?

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Top 10 Contributor
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Bruker Employee

Hi Ilya,

I think you need an updated version.  Can you send an email to afm.support@bruker.com to get a link to download the latest? 

--Bede

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Top 200 Contributor
5 Posts
Points 54

Hi,
I need your help to convert the 65536 force curves obtained by PFQNM into ASCII.
Until then, I have always used Nanoscope analysis to extract the curves but unfortunately the number of files is limited to 2000. To process all the curves, I had to do the packet conversion of 2000, which is really very very laborious.
Would anyone have a routine to do the conversion to ASCII of all the curves.
  Thank you in advance for your answer

Your Bruker job reference number: 30151344

Razafitiana

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