Hi @donghuachen,
There isn’t support for significant per-particle magnification correction. Generally this would only be needed when merging datasets of two different pixel sizes; see Ali’s discussion on this topic. If you combined two datasets with two different pixel sizes, it’s generally recommended to process each dataset individually, since often times only one dataset will contribute high resolution information.
Otherwise, if working with micrographs taken at one pixel size, your initial comment is right – you generally only expect to see small magnification discrepancies. So for small magnification discrepancies that are constant over the dataset (e.g. due to microscope anisotropy), there will be an option to estimate and correct for this in the next release of cryoSPARC. The method is described in Zivanov et al. 2020 in section 2.4. The method was developed to correct for anisotropic magnification, and so can only correct for discrepancies of a few percent. But note that this is a global correction – magnification parameters are assumed to be constant for each exposure group, and this is necessary because signal must be aggregated over many particles to estimate for anisotropic magnification. There is no method that I know of that can estimate for individual particle magnifications. The only other thing that comes to mind is estimating per-particle defocus, but I am not too sure if defocus has a measurable effect on particle magnifications.
Best,
Michael