neurons to include in the analysis

[adezfouli]

The neurons that should be included in the analysis are mentioned in _phy_annotation.npy with values greater than 2. There is also a list of included neurons in steinmetz-et-al-2019/behavior/inclusionData/neurons/. Which criteria is the best one to use?

[adezfouli]

This might be answered in the documentation here:

included.npy [logical] (nTrials) Importantly, while this variable gives inclusion criteria according to the definition of disengagement (see manuscript Methods), it does not give inclusion criteria based on the time of response, as used for most analyses in the paper.

[AngCamp]

Not sure if you have found this out yourself yet but the spikes https://github.com/nsteinme/steinmetz-et-al-2019/wiki/data-files there is a variable clusters._phy_annotation.npy which has human rated quality of the spikes, rating them from 1-3, basically only use those rated as 2. Go to that github url above and give it a read, it will clear a bunch of stuff up.

[adezfouli]

@AngCamp Thanks!