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kwikteam / phy-contrib

[This repository is archived, will be deprecated after the release of phy 2.0]
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Issue displaying data with a left out channel #157

Closed chris-angeloni closed 6 years ago

chris-angeloni commented 6 years ago

I've sorted some data in KiloSort, but noticed that I have a bad channel that KiloSort was finding a lot of clusters on, sometimes merging those clusters with real spikes that I'd like to pull out. To get around this issue, I got KiloSort to not include one of the channels using the connected variable in the channel map. In the end, KiloSort runs without any issues. However, when I try to manually correct clusters in Phy, it looks like something has gone wrong:

noisy_channel_excluded

Namely, if I look at the waveforms of each cluster, there are no spikes, just flat noise (pic above)

However, I know some channels have spikes on them, so if I select a channel with spikes and look at the templates fit by KiloSort, it looks like they fit some spike waveforms!

noisy_channel_excluded_temp

BUT, if I look at the waveforms fit to these templates, there's nothing in the raw data:

noisy_channel_excluded_wavf

It seems as if Phy is not using the right spike times or that the channel map has potentially been mixed up when excluding a channel (ie. the Phy channel numbers go from 0 to 14, but maybe they should go from 0 to 15, excluding the bad channel?).

In params.py there are 16 channels, but only 15 are displayed? Maybe this mismatch is the issue?

Any suggestions?

rossant commented 6 years ago

Are you using the development version? Several bugs were fixed including possibly this one.

chris-angeloni commented 6 years ago

Yes, I am. I tried another recording and I don't seem to have this issue...