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Asking better solutions to large amplitute noise, wrongly merged clusters in Kilosort3, and better guide in paramters #381
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Update 20210427: I've been reading though the issues and gaining some knowledge. Like, the parameters "momentum","sigmamask" are less useful to adjust: first component of "Th" is important for spike detection, second component is important of cluster purity. But I still have no progress in improving my results. I found more examples of unacceptable, weird results: Example 20210427-01: dirty cluster This is example is different from the example above, because that one takes different waveforms in different channels to be from one unit, but this one cannot even found a pure waveform cluster, waveforms are heavily polluted and they are still marked as good. Example 20210427-02: spike waveforms get truncated(wrong spike detection time) |
Example 20210427-04: dirty cluster compared to the example in 20210427-01, I increased lam to 50. I felt that in general, bigger lam seems to have a positive effect, with more truly good clusters. |
hey @Tywang-720 I'm having same issues here, what is your ultimate solutions? |
Hi there, I'm using Ks3, but I found some of my results look a bit funny.
I'm new to Kilosort and phy, and I would be very grateful if someone could look at my results and offer any advice. Like, where did I mess up, how could my results be fixed, etc.
Example 1, about messy cluster:
As I understand it, when I select a cluster in the cluster view in phy, the waveform view shows all the waveforms in that cluster.
But, the waveforms in the picture below look quite different to me, and I'm confused how to fix it by setting Kilosort parameters (like, setting more serious criteria, which parameters are more relevant to this situation?).
Large amplitude noise in the cluster:
Sometimes I found the waveforms get polluted by large amplitute noise. It could be quite severe in some clusters (and they are marked as good nonetheless).
Could Kilosort automatically remove these noises from the cluster? We got tons of data and few hands, manual curation seems to be impractical.
How to tune the parameters in Ks3:
In the above results, I didn't change much default parameters of Kilosort, except the high pass filter and batch size:
ks.ops.fshigh = 300;
ks.ops.NT = 16*1024+ ks.ops.ntbuff;
other parameters are like:
I'm currently wondering, how should I adjust ops.sigmaMask, ops.whiteningRange according to the design of my own probe?
Also, What is ops.lam(amplitute penalty() doing?
If ops.AUCsplit and ops.lam is no longer useful in Kilosort3 as indicated in GUI, then what parameters should I tune first to fix incorrectly merged clusters?
It would be of great help if there could be a detailed document showing the visualized results under specific parameters, to help people understand their behavior.
Thanks!
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