Using phy for the first time

Matheus Oliveira

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Mar 8, 2022, 4:40:20 AM3/8/22

to SpyKING CIRCUS

Just a basic question, I am running spyking-circus in windows wsl2, it runned all way through in my file, but I dont know how to visualise it. These are the files generated.
How to I run phy to manual check the clusters? I have attached my params file.

OUTPUT files:
HUMAN216session1_151106_1545014_channels
HUMAN216session1_151106_1545014_channels.basis.hdf5
HUMAN216session1_151106_1545014_channels.clusters-merged.hdf5
HUMAN216session1_151106_1545014_channels.clusters.hdf5
HUMAN216session1_151106_1545014_channels.overlap.hdf5
HUMAN216session1_151106_1545014_channels.result-merged
HUMAN216session1_151106_1545014_channels.result-merged.hdf5
HUMAN216session1_151106_1545014_channels.result-merged.params
HUMAN216session1_151106_1545014_channels.result.hdf5
HUMAN216session1_151106_1545014_channels.templates-merged.hdf5
HUMAN216session1_151106_1545014_channels.templates.hdf5

best

Matheus

HUMAN216session1_151106_1545014_channels.params

Pierre Yger

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Mar 8, 2022, 4:45:07 AM3/8/22

to Matheus Oliveira, SpyKING CIRCUS

To export for phy, simply do

>> spyking-circus YOURDATA.dat -m converting

Then

>>circus-gui-python YOURDATA.dat (or circus-gui-matlab without converting if you want to have the matlab GUI)

See documentation https://spyking-circus.rtfd.org

Best

Pierre

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Matheus Cafalchio

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Mar 16, 2022, 7:26:06 AM3/16/22

to Pierre Yger, SpyKING CIRCUS

Hi Pierre, how to extract the information back to python after clustering and choosing the best units manually?

Best

Matheus Cafalchio, PhD

Research Fellow - School of Medicine

Trinity College Dublin

Pierre Yger

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Mar 16, 2022, 8:24:15 AM3/16/22

to Matheus Cafalchio, SpyKING CIRCUS

What do you mean? After manually sorting the data with phy? Then everything is saved as python arrays, in yourdata/yourdata.GUI/ and you should have a look to the phy website to know how to recover the structures (time steps, cluster numbers, templates). Hope this helps