Question about event output

[Alex Hoffman]

We've recently begun to use this program more in the lab---really useful!

My question is about the 'Features' output (text file). There are no headers, so I'm trying to decipher what each of the 10 columns indicates. I assume rise, decay times, amplitudes, etc.  but would be helpful to know what each one is.

Thanks,

Alex Hoffman, Ph.D.

NIH/NIDA

  

[Eventer Neuroscience]

Dear Alex,

Thanks you for posting your message!

Information about the features is currently only documented within comments in the source code since it isn't intended for users to read. The values in the features.txt are only intended for internal use and the way some of these features are calculated from the data are quite quick and dirty (e.g. t50 and auc)... but this works fine for it's purpose as a feature set for the machine learning. Nonetheless, you can find the information in the source code file eventer.m, which is here:

https://github.com/acp29/eventer/blob/master/base/eventer.m

% Description of features

% 1) tpeak: time-to-peak

% 2) t50: duration of event above half-maximum amplitude (approximates FWHM)

% 3) tdecay: duration of event post-peak above half-maximum amplitude (approximates decay half-life)

% 4) auc: area-under-curve of the event

% 5) skew: skewness metric for the distribution of the event sample points around the baseline

% 6) ampl: event amplitude calculated from template fitting

% 7) r: correlation coefficient of the template fitting

% 8) rstdev: standard deviation of residuals from the fit

% 9) before: time from preceding event (truncated)

% 10) after: time to next event (truncated)

I personally would not report this info or use this information for anything, partly because of the quick and dirty calculations, and partly because the features will include all 'events' (whether or not they were classified as events by the machine learning). If I wanted to get the above features to document your results, I would get them from the averages documented in the summary.txt file in the ALL_events output folder. If I wanted properties of individual events (like amplitude or interevent interval of individual events), I would get them from the text files in the txt directory from that folder. For features other than those (e.g. rise, decay etc), I would load the event_data data file (I think the default is abf format at the moment) in your favourite general purpose electrophysiology data analysis software (my favourite is Stimfit).

Hope this helps. Was your question more out of curiosity or did you have specific purposes for the feature set?

Best

Andy

--
You received this message because you are subscribed to the Google Groups "Eventer Neuroscience Support" group.
To unsubscribe from this group and stop receiving emails from it, send an email to eventer-neuroscience...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/eventer-neuroscience-support/c30f4380-7cb7-4ba4-b45a-71b34bd0cb86n%40googlegroups.com.

[Alex Hoffman]

Thanks for the detailed response. I primarily was interested in the area measurement, since we are trying to do some analyses involving total charge (area).; for example, getting the Integrated charge over a given period for EPSCs or IPSCs to calculate E/I balance. 

We have used WinWCP and WinEDR quite a bit for many analyses before. So if I follow you, it sounds like we can import the events themselves (as .abf) into say, WCP and then use that to analyze to get AUC or rise/decay, etc? I was wondering how to examine each event for verification anyway, this sounds like the way to do it. Will give it a try! 

Thanks again,

Alex

[Eventer Neuroscience]

Yes that sounds like a good idea. You can change the output file format on the output tab.

BTW, how are your events being classified at the moment (i.e. what is the setting of the 'Event Criterion' on the Detection tab?). If you train a machine learning model, and use that to classify your events you can reduce the frequency of false positive detections.

Best

Andy