Loading files with Neuralynx loader

Share icon

Thu, 01/27/2011 - 06:33 am

Dear all,

I´m trying to load .ncs files from a Neuralynx amplifier into IGORPro and I want to analyse synaptic currents with NeroMatic. In my special case the Patch Clamp trace is recorded with a npi amplifier but gated through the Neuralynx amplifier, therefore the files are .ncs files.
I´m completely new to IGORPro software and NeuroMatic as well. I used the Neuralynx Loader to load the files into IGORpro, but somehow NeuroMatic can´t show this traces because it´s not a pclamp file.
It would really help me if anyone is working with .ncs files and can tell me how to load them and also give me some hinds for analysing them.

thank you in advance and greetings from germany,

koisl
I looked at the information on the file format here: http://www.neuralynx.com/static/software/NeuralynxDataFileFormats.pdf It seems to be pretty straightforward. It appears that it is simply an ASCII header followed by some binary information about the number of samples and the channel recorded, then it just has an array of data samples.

I don't know about the header- perhaps it is human-readable and you can figure it out by reading it.

According to the link above, there is a 64-bit integer giving a time stamp in microseconds, followed by a 32-bit integer giving the channel number, a 32-bit integer giving sample frequency, and a 32-bit integer giving the number of samples. These are followed by an array of 16-bit integers that are the data.

You should be able to load this using the Load Binary Data item from Data->Load Waves menu. You will need to figure out the number of header bytes; I think the number of samples is redundant, as GBLoadWave (the module that implements Load Binary Data) can be told to simply read to the end of the file.

John Weeks
WaveMetrics, Inc.
support@wavemetrics.com

January 27, 2011 at 09:56 am - Permalink

I think your problem is that you're loading the data into Igor fine using the Neuralynx loader, but NeuroMatic isn't recognizing those data waves as ones that it can analyze. That's probably because NeuroMatic stores some information about the data in the waves that it needs to have in order to properly analyze them (eg. signal gain) and possibly also because it expects a certain organization of the data waves. You might want to contact the author of NeuroMatic (Jason@ThinkRandom.com) and see if he has any recommendations for the best way to have NeuroMatic "recognize" your data waves and allow you to analyze them.

January 27, 2011 at 02:10 pm - Permalink

Thank you all for your help.
I´m trying to reach Jason.
Hopefully he might know how to handle the files.

cheers,

Koisl

January 31, 2011 at 02:40 am - Permalink

Hi,

Howard wrote the original Neuralynx loader a long time ago, but I've been updating the project since then. In fact, I load/save Neuralynx files in Igor every day, so hopefully I can help. I can tell you that if you use the Neuralynx loader and load the .ncs file, it is definitely in Igor as an igor wave. I don't know Neuromatic well, but if a neuromatic has a mode that will allow you to work with an Igor wave, as opposed to some other file format, you should be OK. So first, check to make sure that after you have loaded the .ncs file, that it is present in Igor. You can check the Data Browser to see if it was loaded. Then ask Jason how you deal with a wave of synaptic current that is already successfully loaded into Igor.

Rick

February 3, 2011 at 11:56 am - Permalink

check if your are placing the waves in the correct folder in Neuromatic, once you do that just put the prefix of your waves in the prefix menu.

February 22, 2011 at 01:19 pm - Permalink