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Russell Jarvis
@russelljjarvis
Hi Werner, I am also wondering what to do with the 'stim_start', and 'stim_end' dictionary keys if there is no stimulus in the period you are measuring spiking? For-instance I have a signal from an off type Retinal Ganglion cell which spikes spontaneously. A negative current injection has been applied to the signal, however the membrane potential recording has been broken down into 4 different time blocks, which are each analysed individually. The fourth time block has no stimulus, so how can I assign the keys 'stim_start', and 'stim_end' a zero value without causing an error?
Werner Van Geit
@wvangeit
hi @russelljjarvis, did you try to set the stim_start to 0, and stim_end to the max time in the trace ?
This should normally work, let me know if it generates errors for a certain feature
Russell Jarvis
@russelljjarvis
Okay sure. No I have not tried that yet.
Russell Jarvis
@russelljjarvis
I was just thinking that it would be cool if you were not forced to describe stim_on and stim_off keys if the recording is kind of stimulus agnostic.
Werner Van Geit
@wvangeit
would make sense indeed. if you want you create a github issue for it, otherwise I could also do it.
Russell Jarvis
@russelljjarvis
Yes, and sorry that I have not yet addressed the other issues I raised on github issues RE: testing eFEL outside of its directory. I am doing am finishing up an internship and my priorities have shifted recently. I will get back to it soon however.
Werner Van Geit
@wvangeit
np
Russell Jarvis
@russelljjarvis
This message was deleted
Sverre Grødem
@Sverreg
image.png
Not sure if this chat is alive, but I'm having an issue with incorrect peak indices (they are slightly off..). Can anyone help?
In the submitted example blue lines are peak_indices, red lines are AP_begind_indices and the green horizontal line is the peak voltage of the first spike.
Sverre Grødem
@Sverreg
(Fast-spiking cortical PV cell, ~360HZ firing)
Werner Van Geit
@wvangeit
yes, it is alive :-)
did you by chance already try to change the interpolation frequency of eFEL
eFEL has a fairly low default interpolation frequency, with fast spiking cells this could possibly generate problems
Sverre Grødem
@Sverreg
Great! No i did not, where do I change this?
Werner Van Geit
@wvangeit
you can call efel.setDoubleSetting('interp_step', 0.01) to e.g. change the step to .01 ms
(default is 0.1)
Sverre Grødem
@Sverreg
image.png
Great, seems to have fixed the peak indices. But strangely the begin_indices are now off on the 2nd and third spikes. Any clue?
Raising the derivative threshold some more (15 -> 18) took care of that!
Werner Van Geit
@wvangeit
ok, great :-)
yeah, the derivative threshold would be sensitive to the interpolation frequency
Sverre Grødem
@Sverreg
Thanks for the quick response, I was trying lots of silly things as I didn't find this interp_step anywhere. Is there a list of these double settings somewhere?
Werner Van Geit
@wvangeit
not sure it's in the documentation (it obviously should :-)). But the list is here: https://github.com/BlueBrain/eFEL/blob/master/efel/api.py#L74
Sverre Grødem
@Sverreg
I could not find it but that is no guarantee. Thanks for the link!
Sverre Grødem
@Sverreg
Hi again @wvangeit, when I stimulate these fast spikers repeatedly the amplitude of the spikes gets pretty small, and the peak of spike might be as low as 10-20mv. In these instances the feature ['Spikecount_stimint'] no longer gives the full number of spikes. Changing efel.setDoubleSetting("min_spike_height", 10) does not seem to do anything? Is there a different doublesetting for spikes that I can't find?
To avoid confusion: the amplitude of the spike would not be 10-20, but the peak of the spike is at +10-20 mV.
Werner Van Geit
@wvangeit
is it possible for you to trace such a trace ? (to upload it, you could create an issue in the github repo)
Sverre Grødem
@Sverreg
Sure :)
Sverre Grødem
@Sverreg
Hi again. Are anyone here aware of libraries for analyzing voltage clamp experiments? Such as EPSC detection? Or does EFEL have this and I can't find it?
Werner Van Geit
@wvangeit
Hi @Sverreg , eFEL is indeed not really made for detection of EPSCs. It 'might' work, if you put the spike detection really low (and if your voltage trace is fairly flat), but in general I think it's better to use some other code for that.
Sverre Grødem
@Sverreg
Yeah I figured, just wanted to check if anyone has developed that code before I get on it myself.
(In python)
Sverre Grødem
@Sverreg
Hi. How should use of eFEL be cited in a paper?
Werner Van Geit
@wvangeit
hi, there are two option at the moment
in the bluepyopt paper https://www.frontiersin.org/articles/10.3389/fninf.2016.00017/full#B5 we cited it as a url
Blue Brain Project (2015). eFEL. Available online at: https://github.com/BlueBrain/eFEL (Accessed February 16, 2016).
another option is to use Zenodo
but for that one I noticed I have to correct the author list
but I've a permission problem, I'm contacting the Zenodo helpdesk for that
Sverre Grødem
@Sverreg
thanks, I'll check back here in a little while then.
Any preference for which citation to use? Zenodo?
Werner Van Geit
@wvangeit
I'd say Zenodo would be better, but didn't get reply yet
Hassan
@Hassan2060
Hey Werner, I wanted to get some subthreshold features such as "ohmic_input_resistance" but after giving the votage traces i get the error that it needs the "stimulus_current" although both channels are in my traces. do you have any suggestions of how I could get my subthresh properties correctly?
Werner Van Geit
@wvangeit
hi @Hassan2060
You actually need to provide a float with the value of the stimulus current
here is an example on how to do that: