MouseLand
waveform duration, minimum firing rate and high pass filter cutoff
Feature you'd like to see:
Hi there, how can I modify the three parameters in the heading - waveform duration for unit detection, minimum firing rate and high pass filter cutoff?
Additional Context
We are using custom made probes and record brain stem neurons. These cells sometimes have a slower firing rate (lower than 0.5 ms) and some wider waveforms. Also, there are no clear indication of where to find the high pass filter cut off.
Even though I understand that default values are default from experience, I'd like to be able to modify these settings or at least clearly see them.
Waveform duration is determined by nt. The default value of 61 (number of bins) corresponds to around 2ms for a 30 kHz sampling rate. High pass filter cutoff is currently hard-coded at 300 Hz, but I'll make a note to add it as configurable parameter. I'm not aware of any explicit minimum firing rate, but I'll ask @marius10p how that might be addressed.
I confirmed with Marius that there is not an explicit firing rate requirement anywhere in the code. There is however an implicit requirement that "good" units have a minimum number of spikes, which comes from a combination of several variables. The best way to address that for special cases like this would be to do your own post-processing on the sorting results to label cells as good or not and replace KSLabel.npy. I put a tutorial notebook with more explanation for that on the todo list.
Hey @jacobpennington , thanks for the replies. I think you've meant 2 ms and not 2 s in your first comment. I have found the 300 high pass in the source code, thankfully that is the value we would like to use ;) For the firing rate, I have done some spike sorting and I see units with very low spike rate as well in the output of ks4, so this seems to work good.
I think to be future proof we should close this suggestion it when the high pass filter is implemented as a configurable parameter.
@jacobpennington Just stumbled upon this discussion and I was wondering if it was fixed. I saw in the codebase get_fwav doing some hardcoded 300Hz highpass filtering but I don't see it being used anywhere. So I'm hoping it was fixed and this is a function to be deleted maybe?
https://github.com/MouseLand/Kilosort/blob/6684aca018b80e6ba8f79cf8fd1084c7defaa8b8/kilosort/preprocessing.py#L72-L94
Yes, this has been fixed. get_fwav is unused, look at get_highpass_filter.