new version of kilosort (4) _ all in python.

[Aryo-Zare]

You may have already been informed, yet I wanted to mention a new publication regarding a new version of kilosort :
https://www.biorxiv.org/content/10.1101/2023.01.07.523036v1
"Solving the spike sorting problem with Kilosort"

They mention in the manuscript that the new version is written in python from ground up. And that it will be shown in the current github page of kilosort :
https://github.com/MouseLand/Kilosort

Yet so far there is no code available on github for the new version. So how do they work on it ?

kilosort has a built-in drift correction, but seeminlgy does not have an auto-merge option.
In constrast cicus does not have a built-in drift correction but can automatically merge similar units.

Yet spike-interface can do both drift correction and automatic merging independently.

[alejoe91]

Hi @Aryo-Zare

Thanks for opening up the discussion.

We tried to ask them for the code, with no luck... :(

Indeed in SpikeInterface we now have several ways to do motion estimation and correction (including a similar approach to Kilosort4, which I don't believe has a new method for drift correction, but is a port of pykilosort there).

Our experimental curation module has some functions to automatically merge units, and this is exactly the modular approach that we foresee moving forward, since processing and curation will strongly depend on the type of experiment, probe, brain region, etc..so we need to give a certain level of flexibility there!

[Sachuriga]

just wondering I really like spikinterface it's makes life easier, but I would also want to try the kilosort4. Do we have any plan to implement the kilosort4?

[alejoe91]

Of course, but kilosort4 code is not our yet. As soon as they publish the code we'll start the integration

[Sachuriga]

thanks！！！looking forward to that. Alessio Buccino ***@***.***> 于 2023年10月12日周四 12:49写道：

…

Of course, but kilosort4 code is not our yet. As soon as they publish the code we'll start the integration — Reply to this email directly, view it on GitHub <#1473 (reply in thread)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALY2FQT2L2JI7V3LXVMIUZLX67DLNANCNFSM6AAAAAAWQ55X2E> . You are receiving this because you commented.Message ID: <SpikeInterface/spikeinterface/repo-discussions/1473/comments/7262178@ github.com>