Tutorial: Phase Plate Data

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

Tutorial: Negative Stain Data

Tutorial: EER File Support

Last modified 27d ago

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How to specify phase plate data

Import phase plate movies or micrographs

Jobs and parameters affected by Phase Plate Data

Data type reference chart