You can specify the data was collected using a phase plate, when you import the corresponding movies or micrographs.
When importing phase plate movies or micrographs, use the Phase Plate Data toggle in the
Import Movies or
Import Micrographs jobs to indicate that you are importing phase plate data. Subsequent jobs that use the imported phase plate data, will adjust their relevant parameters accordingly (for more details, see below: Jobs affected by phase plate data).
Import Movies: "Phase Plate Data" toggle will set
Import Micrographs: "Phase Plate Data" toggle will set
Patch CTF Estimation: Enables phase-shift search & refinement
CTFFIND4 Wrapper: Enables phase-shift search & refinement
Note: Cryo-EM data is typically recorded as +1 (dark-on-light) but is often inverted during processing.