O-EM batch size (per class)

[vperetroukhin]

Ah fascinating! Yes – we will update the logic to support < 100 class sizes! One note: have you tried running 3D class on non-subtracted particles but using a focus mask? With a focus mask supplied, our 3D class masking procedure effectively replicates particle subtraction, but may work slightly better if your subtraction is not well aligned.

You can refer to this thread for some discussion on this:

3D classification solvent mask behavior

@vperetroukhin just trying to understand if I am understanding this correctly: The focus-masked region (F*V_k) is added to a volume where the focused region is zeroed out and density outside the focus mask mask from the consensus reconstruction is included ((1-F)*barV)) This is then multiplied by the solvent mask to give the class volume. Is this right? What is the effect of replacing the voxels outside the focus mask with those from the consensus reconstruction, rather than just masking them…