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CryoSPARC Guide
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CryoSPARC Guide
About cryoSPARC
Current Version
Licensing
Setup, Configuration and Management
Hardware and System Requirements
cryoSPARC Installation Prerequisites
How to Download, Install and Configure
Software Updates
Management and Monitoring
Troubleshooting
Deployment Guides
Deploying cryoSPARC on AWS
Processing Data in cryoSPARC
Cryo-EM Data Processing in cryoSPARC: Introductory Tutorial
User Interface and Usage Guide
All Job Types in cryoSPARC
Tutorial Videos
Tutorials and Case Studies
Tutorial: Verify cryoSPARC Installation with the Extensive Workflow (Sysadmin Guide)
Tutorial: User Management
Tutorial: Job Builder
Case Study: Processing EMPIAR-10291 (300 Micrographs) to 3.4Ã… in 1 hour 25 minutes
Tutorial: Negative Stain Data
Tutorial: Phase Plate Data
Tutorial: EER File Support
Tutorial: Patch Motion and Patch CTF
Tutorial: Manually Curate Exposures
Tutorial: Particle Picking Calibration
Tutorial: CTF Refinement
Case Study: Yeast U4/U6.U5 tri-snRNP
Tutorial: 3D Variability Analysis (Part One)
Tutorial: 3D Variability Analysis (Part Two)
Tutorial: Queuing Directly to a GPU
Tutorial: SSD Particle Caching in cryoSPARC
Tutorial: Priority Job Queuing
Tutorial: Data Management in cryoSPARC
Tutorial: CryoSPARC Live Session Data Management
Tutorial: Manipulating .cs Files Created By cryoSPARC
Tutorial: Migrating your cryoSPARC Instance
Performance Metrics
Real-time processing in cryoSPARC Live
About cryoSPARC Live
Prerequisites and Compute Resources Setup
How to Access cryoSPARC Live
UI Overview
Live Jobs and Session-Level Functions
New Live Session: Start to Finish Guide
Tutorial Videos
Performance Metrics
FAQs and Troubleshooting
Cryo-EM Data Processing Explained
Questions and Support
cryoSPARC Discussion Forum
cryoSPARC Blog
cryoSPARC Homepage
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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.
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Tutorial: Negative Stain Data
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Tutorial: EER File Support
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Contents
How to specify phase plate data
Import phase plate movies or micrographs
Jobs and parameters affected by Phase Plate Data
Data type reference chart