Limit the number of clusters

[PhantomSpike]

Hi,

I find that I get a bit too many clusters and end up having to merge or discard a significant number.

Is there a way to limit how many templates are initialized and used in the optimization process? In Kilosort 1 this was done via the ops.Nfilt parameter.

In Kilosort 2 this parameter also exists under the same name:

ops.Nfilt = 1024; % max number of clusters

However, even though I set it to e.g. 480 (32*15 so still multiple of 32) I ended up with 732 clusters. Is that because in the splitting stage KS2 found that it was better to split these clusters even though it started with 480?

Thanks!

[marius10p]

Probably. What was the output of Kilosort2 towards the end of the optimization? Split units will have a similarity of exactly "1" in Phy.

You can reduce splitting propensity by increasing ccsplit, i.e. making the separation criterion for splitting more stringent.

[Alkohost]

Can I set ops.Nfilt=5 for example if I use 32 channels and sure about maximal number of clusters?

[marius10p]

Yes, but it will still do splits and merges at the end which might increase your number.

[DemetrisS]

Hello

I am having a similar issue with KS3 when running on data from a 24Ch linear probe (Uprobe) - I am ending with >120 clusters, often >200. I have tried changing "ops.Nfilt" with little effect. I have also played a bit with the AUCsplit (using values from 0.5 to 0.99) with little effect on cluster numbers - any advice would be most welcome.

Many thanks
D

[JonathanAMichaels]

ops.Nfilt isn't actually used. It's defined in preprocessDataSub.m:

ops.Nfilt = getOr(ops, 'nfilt_factor', 4) * ops.Nchan; % upper bound on the number of templates we can have

so you would have to change ops.nfilt_factor if you want to set an upper limit.