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cortex-lab / phy

phy: interactive visualization and manual spike sorting of large-scale ephys data
BSD 3-Clause "New" or "Revised" License
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Cluster view gui data #1280

Open ghattasb opened 6 months ago

ghattasb commented 6 months ago

Hey, I'm using kilosort4 with Phy, and I was wondering how to re-generate that Cluster View table used in the GUI using python? mainly I would like to know how you managed to map the clusters to a specific channel since I could not find a file that contains this type of data sorting.

Thank in advance

zm711 commented 6 months ago

@ghattasb,

It's occurring based on loading the amplitudes and channel mapping information. So you could read the source code to figure out how to do it. There will be some functions inside of phy and phylib which you could call by using a phylib model rather than the gui and then get all the values you need. If you want to do that I would recommend heading over to phylib and reading the source code there (unfortunately not a lot of documentation). We also work with the spikeinterface team and they also have ways to do that (you can auto load kilosort data, then find the specific channels). There's more documentation over there currently for how the api works.