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Kilosort templates can be all NaNs #28
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Hi Luke, Thanks for your message!
If a unit has no template waveform, it should be discarded. A try / catch statement will correctly handle this case, but I prefer to handle the specific issue (ie not computing the quality metrics if there is no waveform) because try/catch statements can mask some bugs and make it harder to troubleshoot. Thanks again! Cheers, |
Hi Julie, I am using Kilosort 2.5. This unit does inexplicably have spikes assigned to it. I am also befuddled. I also reran Kilosort but it made the same NaN template.
Thank you, |
How odd! I will modify bombcell to handle this special case. If you can, it might be useful to raise a github issue for Kilosort 2.5. This doesn't sound like normal behavior. |
Hi Luke, |
Hi Julie, Thank you so much! As for the Kilosort side, I found another user who get all NaN templates in the Kilosort Issues. Unfortunately, the source of their problems seems entirely different than mine. I had intended to ask Nick Steinmetz about possible causes in person, but I didn't have the time during the meeting. So I've just raised an issue on the Kilosort page. |
That sounds good! Let me know if you figure it out, I am curious as to what is going on. |
Hi Luke, |
Hi Julie,
Thank you so much! No one ever responded to the issue I raised on Kilosort
2.5. I'm afraid that I may need to bug someone directly or in-person. If I
ever find out why the NaN templates are made, I'll let you know!
Thank you,
Luke
…On Tue, Jan 9, 2024 at 8:21 AM Julie Fabre ***@***.***> wrote:
Hi Luke,
Someone else has run into the same issues as you (github issue #60
<#60>) and I have
integrated changes in the main branch to deal with these abnormal
waveforms. You should be able to change back to this branch and be able to
get any recent updates and feature upgrades.
I'm still confused about why kilosort is outputing these waveforms, but at
least bombcell now handles it by default!
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Luke Bun
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|
Hello Julie,
I discovered that Kilosort is capable of outputting all NaNs for a template. As a result, bombcell will run into an error in "bc_waveformShape" when it tries to index into "max_waveform_value" which is empty.
My working solution is to put a try-catch around where "bc_waveformShape" is called in "bc_runAllQualityMetrics" and continue past the unit with the all NaN template.
I think it would be helpful for bombcell to be able to handle all NaN templates.
Thank you,
Luke
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