How to check for very high firing frequencies.

[Jose Guzman]

Hi,

First of all, thank you very much - again -  for such an excellent piece of software!

I want to test if the spikes of my clusters are physiological (i.e., say, ranges <100 Hz for simplicity). Unfortunately, It's not clear to me how to set the bin size in ISIView or in FiringRateView. I realized that both FiringRateView and ISIView use xmax and xmin in sec. Then, to have the histograms in spikes per second, I would have to 

1) In FiringRateView set n_bins to the duration of the recording in seconds. Thus, I will have to adjust it for every recording duration, but I could see when the firing rate > 100 Hz by looking directly to the y-axis < 100 Hz of the FirinRateView.

2) In ISIView is more simple, since I will have to look for the number of bins < 0.1, independently on how large is xmax. However, I would appreciate if to know what is if bin number is set in the xmin - xmax interval, or all over the recording time. 

Thank you very much in advance for your comments!

By the way, in the CorrelogramView, what is the little number on top of the horizontal line of the histogram? It's overlapped with the time label located on the right x-axis. I would recommend moving that number to say 3/4th of the window size (for 100 ms, write in in 75 ms).

[Cyrille Rossant]

It seems these views lack a set_bin_size() function, would that solve the problem for you?

Cyrille

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[Jose Guzman]

Yes, I think setting the bin size (in ms) in the ISIView would be useful. In CorrelogramView, the bin size is documented to be in milliseconds. In ISIView, it is possible to set the bin size (alias :isin), but I am not sure if the number is for the whole dataset, or only for the limits given in the plot.

Thanks!

Jose 

On Monday, 5 August 2019 18:33:07 UTC+2, Cyrille Rossant wrote:

It seems these views lack a set_bin_size() function, would that solve the problem for you?

Cyrille

Le mer. 31 juil. 2019 à 13:21, Jose Guzman <sjm....@gmail.com> a écrit :

Hi,

First of all, thank you very much - again -  for such an excellent piece of software!

I want to test if the spikes of my clusters are physiological (i.e., say, ranges <100 Hz for simplicity). Unfortunately, It's not clear to me how to set the bin size in ISIView or in FiringRateView. I realized that both FiringRateView and ISIView use xmax and xmin in sec. Then, to have the histograms in spikes per second, I would have to 

1) In FiringRateView set n_bins to the duration of the recording in seconds. Thus, I will have to adjust it for every recording duration, but I could see when the firing rate > 100 Hz by looking directly to the y-axis < 100 Hz of the FirinRateView.

2) In ISIView is more simple, since I will have to look for the number of bins < 0.1, independently on how large is xmax. However, I would appreciate if to know what is if bin number is set in the xmin - xmax interval, or all over the recording time. 

Thank you very much in advance for your comments!

By the way, in the CorrelogramView, what is the little number on top of the horizontal line of the histogram? It's overlapped with the time label located on the right x-axis. I would recommend moving that number to say 3/4th of the window size (for 100 ms, write in in 75 ms).

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[Cyrille Rossant]

This is done in the latest version of phy, you now have the following snippets for the ISI view:

:isin 100  # number of bins

:isimax 100  # max bin in ms

:isib 1  # 1 ms per bin

Cyrille

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[Jose Guzman]

Cool, it works a like a charm!

Thanks!

Jose

JoSe GuZmAn • The Guzman Lab
http://www.guzman-lab.com

Tel.:     +43 678 126 70 96 
Email:  jose....@guzman-lab.com