Hi everyone!
Whenever you are inspecting half maps from CryoSPARC, it’s good to remember that we perform no filtering whatsoever – they are exactly as reconstructed from the particle images. As I’ve mentioned in the posts you reference @Joe, unless your reconstruction is very close to Nyquist, the noise from high frequencies will swamp out the signal in your unfiltered half maps. Keep in mind too that, when looking at the whole box like this, the unmasked FSC may be more useful in gauging your expectations.
You can see this effect yourself by taking a reconstruction which has not reached Nyquist (like this one) and comparing its half maps to half maps produced by reconstructing downsampled images (downsampling is, in essence, a lowpass filter). The particles used for this diagram are the exact same particles with the exact same poses, but the lower row is a reconstruction for which the images have been downsampled such that the reconstruction is much closer to Nyquist.
I’m happy to answer any more questions you all have on this topic!
Edit because I forgot to close the loop: in general, the appearance of noise in half maps is expected and is not alone reason to worry about your reconstruction.