Kilosort templates can be all NaNs about bombcell

[lukebun]

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

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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! — Reply to this email directly, view it on GitHub <#28 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AOYXGIMSOCVPSPF6CGNUDE3YNVU7LAVCNFSM6AAAAAA5ICWLJSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQOBTGM3DEMRVGM> . You are receiving this because you authored the thread.Message ID: ***@***.***>

-- Luke Bun Bioengineering PhD Student University of Washington Email: ***@***.***

[Julie-Fabre]

Hi Luke,

Thanks for your message!
I've never seen that before. Which version of kilosort are you using? It doesn't make much sense to me that unit could have spikes times and no template waveform. Just to be sure of what's going on:

• Do you get the error in the bc_waveformShape function?
• What is the unit in question's maximum channel (qMetric.maxChannels(thisUnit)) ?

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.
I can add a check to only select units with waveforms before running bombcell's main loop, and then I suggest you pull that code or implement a similar change rather than having a try / catch statement.

Thanks again! Cheers,
Julie

[lukebun]

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.

• Yes, the error is in bc_waveformShape. Specifically, line 103 "if max_waveform_value(end) > 0." Because max_waveform_value is a 1x0 empty array, it can't index into it.
• The maximum channel of the unit is 1.

Thank you,
Luke

[Julie-Fabre]

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.

[Julie-Fabre]

Hi Luke,
I've created a branch to deal with waveforms that contain NaNs. By default, any of these units will not be classified (since it does not make any sense for waveforms to be NaNs). Here is the branch: https://github.com/Julie-Fabre/bombcell/tree/waveform_nans
Let me know if you run into any issues.
Have you had any luck figuring out what's going on in kilosort to create waveforms that are all NaNs?

[lukebun]

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.

[Julie-Fabre]

That sounds good! Let me know if you figure it out, I am curious as to what is going on.

[Julie-Fabre]

Hi Luke,
Someone else has run into the same issues as you (github issue #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!