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
Performance Metrics
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
Workflows
Import
Motion Correction
CTF Estimation
Exposure Curation
Particle Picking
Deep Picking
Particle Curation
3D Reconstruction
3D Refinement
CTF Refinement
Variability
Postprocessing
Local Refinement
Helical Reconstruction (BETA)
Utilities
Job: Volume Tools
Job: Sharpening Tools
Job: Validation (FSC)
Job: Volume Alignment Tools
Job: Particle Sets Tool
Job: Exposure Sets Tool
Job: Symmetry Expansion
Job: Generate Micrograph Thumbnails
Job: Exposure Tools
Job: Cache Particles on SSD
Job: Remove Duplicate Particles
Job: Check for Corrupt Particles
Job: Reassign Particles to Micrographs
Simulations
Tutorial Videos and Webinars
Tutorials and Usage Guides
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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Job: Volume Tools

Description

Use this job to one or more of the following operations on an input Volume or Mask:
  • Upsample/Downsample
  • Crop
  • Add soft padding
  • Flip handedness
  • Lowpass Filter
  • Dilate mask
  • Invert mask
  • Threshold mask
  • Clip a mask along the z-axis (for helical refinements)
  • Convert between mask and volume

Input

  • A map volume or mask

Common Parameters

  • Type of input volume: Choose whether to use the volume or mask input slot. The volume operations are only applied to the input at the selected slot
  • Type of output volume: The type of the output once the Volume Tools operations are complete. Can be the same or different from the type of the input volume

Output

  • The edited input map volume or mask

Common Next Steps

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Job: Sharpening Tools
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Contents
Description
Input
Common Parameters
Output
Common Next Steps