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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.
Russell Jarvis
@russelljjarvis
I am still interested in making a julia API for EFEL. To this end it would be better if the EFEL core was written in regular C and not cpp. Do you think that the EFEL core strictly depends on many CPP only features? Would it be hard for someone to write it in regular C?
Werner Van Geit
@wvangeit
@russelljjarvis we're actually rather thinking of rewriting the entire efel in Python. Is it possible to make a julia API for a python library?
Russell Jarvis
@russelljjarvis
PyCall is julias way of interacting with python. PyCall is so slow that it is not worth going that route. I am guessing the newer version of efel might use cython? It would actually be faster to make a command line argument version of efel and call that from julia as a shell process. Have you seen how numba.jit and vectorize can speed up regular python a lot?
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Aman Aberra
@Aman-A
Hi I was wondering if AHP_time_from_peak_last and AHP_depth_last features were removed in more recent version of eFEL, and if so, could they could be added back in some way? I'm using version 3.1.90 and they don't seem to be available
Werner Van Geit
@wvangeit
Were they ever there? They are in the 'requested features' section of the doc. I can't find them in the repo.
If you need these specific ones we can implement them, it's best to create an issue for it on the eFEL website
1 reply
Russell Jarvis
@russelljjarvis
@wvangeit Regarding the PR, I am currently applying for postdocs and other jobs. I will get back to doing it in another 2weeks. Also it looked basically done except for tox.ini build errors I didn't undertand. It might be worth me starting a new PR so its easier to visualize the difference.
EC-byte
@EC-byte
@wvangeit Hey Werner. I'm following along with the example notebook on the eFEL github, I'm calling the efel.getFeatureValues([trace]...) function but I'm running into an issue. My data comes from voltage imaging, and so the default threshold is not within the range of my spikes. Is there a way to pass a new threshold to this function? I've tried efel.setThreshold() to no avail. Thank you
EC-byte
@EC-byte
Screen Shot 2022-03-20 at 2.25.24 AM.png
Werner Van Geit
@wvangeit
One thing I could suggest is maybe to rescale the y-axis a bit so that it 'looks' like mV? Otherwise, could you maybe create an issue on the efel github website with a reproducible example (we mostly need the raw data)? Then we can have a look.
to be sure, pinging @EC-byte