Value of amplitude

[Lorena-J]

Describe the issue:

Hello! I have been testing ks4 with a single shank probe and comparing the rating with ks 2.5 and 4 there is a big difference in the amplitude values and I don't know what are the units of this amplitude in ks4:

[jacobpennington]

Hello,

Kilosort4 does not save amplitudes in exactly the same way that past versions did, so there will be differences. Please see my last reply in #632 for details. However, they should not be nearly as large as you've shown in that screenshot, that's many orders of magnitude larger than expected. Are you using the latest version of Kilosort4? There were updates to the amplitude calculations not too long ago.

[Lorena-J]

I am using the lastet version, but is there a problem with other parameters, or can I do the classification and calculate the amplitudes myself?

[jacobpennington]

I would assume there are issues with other parameters, but I can't tell without seeing some screenshots and/or printouts. To give you an idea, the scale of the 'amp' column (which is computed by Phy based on the templates that Kilosort learns) is around 100-500 for our sample Neuropixels 1 dataset. That scale is expected to be different for different datasets, but that big of a difference seems very unlikely.

Can you please post a screenshot of what the full GUI looks for you prior to sorting, including the "extra settings" window?
I.e. something like this:

Copy-pasting the full print output generated during sorting would also be helpful, if it's feasible to run it again.

[Lorena-J]

yes, sure, I'm doing the analysis with a single shank probe, it has 64 channels, I don't know why but channel '0' is not represented in the probe view, here are the screenshots:

thank youu!!!

[jacobpennington]

If a channel is not showing up in the probe view, then it's either not included in the probe file or the coordinates were entered incorrectly (i.e. possibly overlapping another contact so that you can't see it). That could cause some of the preprocessing variables to behave unexpectedly, so you would need to fix your probe file first.

[jacobpennington]

Closing this for now, if you still encounter problems after updating the probe file please let us know.