Tutorial: Phase Plate Data

Learn how to work with Phase Plate data in CryoSPARC.

How to specify phase plate data

You can specify the data was collected using a phase plate, when you import the corresponding movies or micrographs.

Import phase plate 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).

Jobs and parameters affected by Phase Plate Data

  1. Import Movies: "Phase Plate Data" toggle will set mscope_params/phase_plate to 1 (True)

  2. Import Micrographs: "Phase Plate Data" toggle will set mscope_params/phase_plate to 1 (True)

  3. Patch CTF Estimation: Enables phase-shift search & refinement

  4. CTFFIND4 Wrapper: Enables phase-shift search & refinement

Data type reference chart

Data Type

Data Sign





Negative Stain



Note: Cryo-EM data is typically recorded as +1 (dark-on-light) but is often inverted during processing.

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