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Noisy clusters #80
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The big vertical lines on the waveform view suggest that you have some very
large-amplitude artifacts. You might try detecting these with a simple
threshold and then removing that part of the data, then run again. If you
don't think that the artifacts impacted your sorting results much, though,
then you can simply "split" them out in your phy gui. Looks to me like that
would be fine for the example cluster you're showing.
…On Sun, Aug 6, 2017 at 6:43 PM, shihaisun ***@***.***> wrote:
Hi KiloSort team,
A lot of my clusters are noisy following KiloSort spike-sorting. Below is
an example of a noisy cluster (as seen in the feature view and waveform
view).
[image: image]
<https://user-images.githubusercontent.com/30403651/29005595-ab2b533c-7b21-11e7-980f-5c3bef61e582.png>
I changed the maximum clusters in the config file to 128 and left the rest
on default. Can you guys recommend me any setting changes to fix my noisy
clustering issue?
Thank you so much for your time,
Scott
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Hey @nsteinme any nice ways you guys have to run such a filter? Maybe a plugin? |
No, I don't have a method for this - I always run common average
referencing before sorting, which I guess must be removing any such
artifacts that I have. I rarely see problems like this.
…On Fri, Mar 9, 2018 at 2:03 PM, Brendon Watson ***@***.***> wrote:
Hey @nsteinme <https://github.com/nsteinme> any nice ways you guys have
to run such a filter? Maybe a plugin?
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Ah i see. That's a good point. So you create a second binary file that's averaged across channels and then run kilosort on that? (also, have you ever tried median filtering?). Thanks |
Yes, I use this function:
https://github.com/cortex-lab/spikes/blob/master/preprocessing/applyCARtoDat.m
No, I haven't tried median filtering...
…On Sat, Mar 10, 2018 at 6:06 AM, Brendon Watson ***@***.***> wrote:
Ah i see. That's a good point. So you create a second binary file that's
averaged across channels and then run kilosort on that? (also, have you
ever tried median filtering?). Thanks
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Thanks! |
I think by "median filtering" people sometimes mean like what matlab's "medfilt1" does - where it takes a running window and replaces each point with the median of the values in that window. Here I'm doing something different: First, for each channel separately, I subtract the channel's median (across all time) from every point in the trace (this step just removes channel offsets, which is a thing with neuropixels probes but probably irrelevant for most probes); second, for each time point separately, I take the median across channels and subtract it from every channel's point. The second step is what people call common average referencing (whether it's a mean or median, probably doesn't matter too much...). I should have made that comment in the function more clear! |
Hi @nsteinme,
|
Hi @nsteinme, I have a question Thanks a lot. Hankyul Kwak |
CAR is automatically applied by kilosort! No need for you to take any
special step. It will exclude any channels you've labeled as bad before
doing the CAR.
…On Thu, Aug 26, 2021 at 10:33 PM HankyulKwak ***@***.***> wrote:
Hi @nsteinme <https://github.com/nsteinme>,
I have a question
Firstly, when we start kilosort, it begins with preprocessing. I was
wondering if the preprocessing includes applyCARtoDat.m ?
Secondly, if it doesn't include applyCARtoDat.m, do I have to run kilosort
following applyCARtoDat.m ?
Thanks a lot.
Hankyul Kwak
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Hi KiloSort team,
A lot of my clusters are noisy following KiloSort spike-sorting. Below is an example of a noisy cluster (as seen in the feature view and waveform view).
I changed the maximum clusters in the config file to 128 and left the rest on default. Can you guys recommend me any setting changes to fix my noisy clustering issue?
Thank you so much for your time,
Scott
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