Hi @msateryster,
At the moment we don’t have any jobs integrated into CryoSPARC that accomplish this workflow (the most analogous thing would be a version of 3D Variability Display that works with the latent variables from 3D Flex). See related request here. In short, the best way this can be done is via CryoSPARC Tools which could for e.g. be used to isolate or cluster particles based on their latent values, and then output separate stacks to an External Job in CryoSPARC for further reconstruction.
Best,
Michael