The message
may be triggered when the new Remove duplicate particles option in 2D classification is used with particles picked in older versions of CryoSPARC.
For particles picked in CryoSPARC versions older than 4.4.1, we recommend disabling the Remove duplicate particles option in 2D classification. The standalone Remove Duplicate Particles job type, for which one can specify a custom Micrograph pixel size, can instead be used after the 2D classification job.
If one anticipates extensive use of 2D classification in a project with pre-v4.4.1 particles, it may be preferable to re-pick particles in v4.4.1 for use in 2D classification.