5. Automated "good"
NOTE: This Wiki is kept here for reference for previous versions of Kilosort. For updated information about Kilosort4, please refer to kilosort.readthedocs.io instead.
We feel good enough about the output of Kilosort2 to recommend whether a unit is "good" or not. You will see this recommendation in the Phy GUI, and you can take it from the Matlab variable rez.good.
This step is likely to change the most as we receive more feedback from users. Currently good-ness is exclusively a measure of how many refractory violations a cluster has within a +/-1.5ms period compared to how many you'd expect from the tails and shoulders of the autocorrelogram. The central 1ms of the 3ms interval is excluded, because any duplicates there are likely rare artifacts. The proportion of refractory violations is also an approximate estimate of the proportion of contaminating spikes from other clusters noise, and we added this information to Phy as well.
In the near future, we will also add a shape classifier to detect good units, just to make sure noise is never labelled "good".