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Batch processing C-AFM I-V data

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joevogel posted on Wed, Nov 24 2010 5:34 AM

Bonjour,

 

I have the following problem. I am using the contact mode TUNA mode of the MM8 with NSV controller and NS 8.1 software.

I several I V curves by the point and shoot routine. I want to process this huge amount of data further with a common software like origin, matlab or excel.

 

I would like to know if there is a possibility to batch process the export of the ramp curve into asci files.

Is the a possibility to read out the ramp files from point and shoot directly with a common software like origin or excel?

 

Thank you very much.

 

Jörn-Oliver Vogel

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Bruker Employee

Hi Oliver,

I'm assuming that you are looking to do a binary export since the ASCII export can do multiple channels for approach and retract and it can do this for multiple files at once (from the browser as I described).

There is some general file format information for reading the raw files (which is valid for force curves) in the appendix sections A3, A5, A7 of the Nanoscope 8.10 manual that you mention.  Be sure that you understand the ciao parameters since that is how you scale the binary data.  A few other things:

  1. The ramp channel data (Z position) is not stored for each point, instead the header describes the range and number of samples, so you can calculate the Z position for each of the data points
  2. Each channel has a separate header section or "Ciao force image list" where offsets, datalengths, and data types are described
  3. The approach (trace) and retract (retrace) data for each channel is stored together as 16bit integers with trace data first, then retrace data.
  4. The order of the data is a little weird -- both approach and retract data are stored starting with the most extended position, so the approach data is in reverse time order.  If you are using triggering, the system sometimes reaches the trigger point before the requested ramp size is reached.  If that happens, the file data is filled with a special number (I think it is the most negative number) to indicate that it is not real data.

I hope that helps!

--Bede

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Suggested by Bede Pittenger

Hi Jörn-Oliver,

You can do batch exporting of ramp files to ASCII in either Nanoscope or Nanoscope Analysis by

  1. selecting all of the files you want to export (with shift-click or ctrl-click) in the browse view 
  2. right click to open the contex menu
  3. choose Export>ASCII...
  4. This will generate a bunch of text files that can be read by Excel or whatever else you want to use

If you are using matlab, you might consider reading the files directly from the binary to avoid the export step, but the downside is that you would need to parse the text header to find out the scaling factors to convert the binary data into metric units.

--Bede

 

Top 150 Contributor
6 Posts
Points 70

Hi Bede,

 

Thank you for your suggestion. I am already using the normal route to export the ascii, but it is quite tiring since it takes a lot of clicks, especially if you are interested in the approach and the retract scan.

Unfortunately there is no documentation on the

 

\*Force file list
\Version: 0x08100000
\Date: 03:06:33 PM Tue Nov 23 2010
\Start context: FOL 

 

file format in the manual NS 8.1 rev C. It just discusses the image data and the force images.

I like to read out the single ramp files, which the Point and Shoot outputs.

I it possible to get a documentation on this?

 

Thank very much

 

Oliver

 

  • | Post Points: 12
Top 10 Contributor
280 Posts
Points 6,219
Bruker Employee

Hi Oliver,

I'm assuming that you are looking to do a binary export since the ASCII export can do multiple channels for approach and retract and it can do this for multiple files at once (from the browser as I described).

There is some general file format information for reading the raw files (which is valid for force curves) in the appendix sections A3, A5, A7 of the Nanoscope 8.10 manual that you mention.  Be sure that you understand the ciao parameters since that is how you scale the binary data.  A few other things:

  1. The ramp channel data (Z position) is not stored for each point, instead the header describes the range and number of samples, so you can calculate the Z position for each of the data points
  2. Each channel has a separate header section or "Ciao force image list" where offsets, datalengths, and data types are described
  3. The approach (trace) and retract (retrace) data for each channel is stored together as 16bit integers with trace data first, then retrace data.
  4. The order of the data is a little weird -- both approach and retract data are stored starting with the most extended position, so the approach data is in reverse time order.  If you are using triggering, the system sometimes reaches the trigger point before the requested ramp size is reached.  If that happens, the file data is filled with a special number (I think it is the most negative number) to indicate that it is not real data.

I hope that helps!

--Bede

  • | Post Points: 13
Top 150 Contributor
6 Posts
Points 70

Thank you very much.

I think that will help me further.

 

Oliver

  • | Post Points: 10
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