Particle normalization in cryosparc

Hi, How exactly does cryosparc normalize the particle images? e.g. std = 1.0
I need to import a particle set, is there a tool in cryosparc to (re)normalize all the particles?

On a related topic, we have two datasets (same sample) from different microscopes whose reconstructions display at quite different grey scale. Is it possible to merge these two datasets?


Hi @zhangrui_wustl thanks for posting
Particles are normalized at the extraction (or local motion) stage. The particles are normalized on a per-micrograph basis (so that variations in ice thickness across a single micrograph are maintained). There is not currently a way to renormalized a imported set of particles.

For particles that are on different greyscales, you can turn on “optimize per-particle scale” in refinement and that should be accounted for. But combining data from different microscopes can have many other issues, mainly if the pixel sizes are slightly different!

Hi @apunjani Thank you so much for the explanation and tips!

Yes, to merge data from different microscopes, the scaling factor between different pixel sizes has to be super accurate. This can be estimated by comparing the respective reconstructions.

Here is another functionality request. It would be great to have a tool to arbitrarily scale a particle set at one Å/pixel value to another, together with a new box size (I understand some value can only be approximated due to integer box size). The current “Downsample particles” function is not so straightforward.