Alteration in kilosort package leads to error using kilosort4

[RichardFav]

Dear Devs,

I recently updated my version of kilosort (from 4.0.37 to 4.1.2) and this caused an error using kilosort4 within the Spikeinterface spike sorter (specifically at Line 310 of spikeinterface.sorters.external.kilosort4._run_from_folder).

I did some digging, and found that the error is due to a change made to kilosort on Sept 17 (MouseLand/Kilosort@42fd52c) whereby "batch_downsampling" is added to the parameter list (see Line 573). This causes the aforementioned error as the function now requires 17 outputs (instead of the 16 listed currently within spikeinterface).

I found a hack solution was to add in an extra ", _" to Line 310 (i.e., ignoring the parameter), although this parameter could also be repurposed for use within the solver - depends on how you want to handle things I guess.

[chrishalcrow]

Hi @RichardFav , this was fixed last week here #4206, but the patch isn't in a release version of spikeinterface yet. So to use it you'll need to install spikeinterface from source (https://spikeinterface.readthedocs.io/en/stable/get_started/installation.html#from-source). Or you could use kilosort 4.1.1. Or keep your hack for now :)

[RichardFav]

Hi @chrishalcrow, thought you guys would be on top of it - my bad for not checking the fixes... Thanks for passing on the info in any case.