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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:
Sverre Grødem
@Sverreg
Is there any setting I can't find for changing the AHP search timing? ie. to change the start of search timing for AHP_depth_abs_slow from 5ms to 2ms?
Werner Van Geit
@wvangeit
no, i don't think it's possible at the moment
if you think it would be useful for you that we implement it, maybe you can create an issue, and I'll assign it to someone
Sverre Grødem
@Sverreg
Will do, thanks!
At 500hz firing 5 ms is a long time.