Rank: 1769 based on 43 downloads (last 30 days) and 3 files submitted
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Forrest Collman

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Company/University
Stanford University

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Professional Interests:
neuroscience

 

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16 Aug 2012 abf2load a version of abfload which is capable of reading abf 2.0 files Author: Forrest Collman abf, action binary file, data import, binary, data export, axon 40 14
  • 4.44444
4.4 | 11 ratings
30 Dec 2009 ReadNVT Reads in a Neuralynx NVT Cheetah binary file into Matlab Author: Forrest Collman neuralynx, cheetah, nvt, binary file, input, binary 2 0
29 Aug 2008 Screenshot double_thresh Function for a simple hysteretic Schmidt trigger on a vector Author: Forrest Collman schmidt trigger, thresholding, signal processing, utilities 1 0
Comments and Ratings by Forrest
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28 Jul 2009 abf2load a version of abfload which is capable of reading abf 2.0 files Author: Forrest Collman

I have fixed the error that was causing JoAnna's problem
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11 Jul 2012 abf2load a version of abfload which is capable of reading abf 2.0 files Author: Forrest Collman Jonas

Hi,

I'm using abf2load for plotting of IV curves from episodic traces.

I'm not very experienced in Matlab. Is there any possibility to extract the clampex comment (which you can manually enter after a each recording) in with abf2load?
I was trying to find it in the code but was unsuccessful so far. Would be nice if someone could give me some advice.

Thanks in advance,
Jonas
29 Jun 2012 abf2load a version of abfload which is capable of reading abf 2.0 files Author: Forrest Collman wjg

Another bug + fix. If you request a subset of channels, you get them in the order listed in the 'channels' argument. However, if you request all channels, they always are returned in the same order as the file, even if the order given in 'channels' is different. The fix is to change line 674 from:

elseif length(chInd)/h.nADCNumChannels<1

to:

elseif length(chInd)/h.nADCNumChannels<1 || any(chInd ~= 1:h.nADCNumChannels)

06 Jun 2012 abf2load a version of abfload which is capable of reading abf 2.0 files Author: Forrest Collman Matthew

@Ryan and anyone else having the empty goodstart problem:

Look at lines 270 through 275. The name of the program that saved the ABF file is part of the file format. If you saved yours in another program, for instance Clampfit, changing 'axoscope' to the name of the program should work (or, for slightly more robustness, adding a second isempty() check). It solved the problem for me, although it's still a messy hack (as the comments in 270 and 272 do, to be fair, point out).
08 Jun 2011 abf2load a version of abfload which is capable of reading abf 2.0 files Author: Forrest Collman Ryan

I have the same problems with the tag section, which I have to comment out. Once I do that, the program works about 80% of the time as opposed to about 30% of the time. I also have issues with the following error:

??? Attempted to access goodstart(1); index out of bounds because numel(goodstart)=0.

Error in ==> abfload at 277
BigString=BigString(goodstart(1):end)';

Error in ==> Converter at 63
d1=abfload(abf);
09 Feb 2011 abf2load a version of abfload which is capable of reading abf 2.0 files Author: Forrest Collman Arthur

Forrest, I ran into a problem with abf files containing tags. When I try to load them I get the following error:

??? The following error occurred converting from struct to double:
Error using ==> double
Conversion to double from struct is not possible.

Error in ==> abfload at 327
Tagsec(i)=ReadSection(fid,TagSection.uBlockIndex*BLOCKSIZE+TagSection.uBytes*(i-1),TagInfo);

The problem seems to be in the line just before (line 325):

Tagsec=[];

This creates an empty double array, but output of the following loop is a struct. Simply commenting line 325 solved the problem for me.

Thanks again for an otherwise great function.

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binary, utilities, abf, action binary file, axon
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Updated   File Tags Downloads
(last 30 days) 		Comments Rating
16 Aug 2012 abf2load a version of abfload which is capable of reading abf 2.0 files Author: Forrest Collman abf, action binary file, data import, binary, data export, axon 40 14
  • 4.44444
4.4 | 11 ratings
30 Dec 2009 ReadNVT Reads in a Neuralynx NVT Cheetah binary file into Matlab Author: Forrest Collman neuralynx, cheetah, nvt, binary file, input, binary 2 0
29 Aug 2008 Screenshot double_thresh Function for a simple hysteretic Schmidt trigger on a vector Author: Forrest Collman schmidt trigger, thresholding, signal processing, utilities 1 0

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