handlig of .prb file

[jrnvndtslr]

I have a custom linear probe, so I need to create my own probe file. In order to do that I want to know how Kilosort interprets the .prb file, but I can't find the code where this happens. Could someone tell me where in the code this happens or what the values in the probe file represent (e.g. electrode site, AD, or ncs (I use Neuralynx))?

[marius10p]

examples here: https://github.com/MouseLand/Kilosort/blob/main/configFiles/createChannelMapFile.m

you can also create it via the GUI.

[jrnvndtslr]

Thanks for the quick response.

I had already found the script you referred to. My question is rather related to how Kilosort knows which channel data (a .ncs file in my case) corresponds to which xy coordinates.

[marius10p]

You need to write your data as an int16 binary file in channel-major order, so ch1 t1, ch2 t1, ch3 t2, ... ch1 t2, ch2 t2,...

[jrnvndtslr]

Ah so if I understand it correctly you're saying that the channelmap variables are matched to channels based on their index? So that would mean that as long as I match the order of my probe map variables to that of my channels the results should be correct.

If I understood that correctly then my next question is what determines the order of the channels. Is it simply the filename?

[marius10p]

Yes, ch1 should be the first row in your binary file, ch2 should be the second row, etc. However, Kilosort won't work with ncs files. You'll have to load the data into Matlab yourself, arrange them in the correct order, and then write them back to a single binary file with the channel order I specified above.

[jrnvndtslr]

Thanks a lot for the help!