In order to be sure that the parameters in configuration file are correct, and before launching the algorithm that will filter the data on-site (and thus mess with them if parameters are wrong), one can use the preview GUI. To do so, simply do:
>> spyking-circus path/mydata.extension -p
The GUI will display you the electrode mapping, and the first second of the data, filtered, with the detection thresholds as dashed dotted lines. You can then be sure that the value of spike_thresh used in the parameter file is correct for your own data.
Once you are happy with the way data are loaded, you can launch the algorithm.
You can write down the value of the threshold to the configuration file by pressing the button
Write thresh to file
In order to quickly visualize the results of the algorithm, and get a qualitative feeling of the reconstruction, you can see use a python GUI, similar to the previous one, showing the filtered traces superimposed with the reconstruction provided by the algorithm. To do so, simply do:
>> spyking-circus path/mydata.extension -r
If results are not there yet, the GUI will only show you the filtered traces
You can show the residuals, i.e. the differences between the raw data and the reconstruction by ticking the button