CryoSPARC Guide
  • About CryoSPARC
  • Current Version
  • Licensing
    • Non-commercial license agreement
  • Setup, Configuration and Management
    • CryoSPARC Architecture and System Requirements
    • CryoSPARC Installation Prerequisites
    • How to Download, Install and Configure
      • Obtaining A License ID
      • Downloading and Installing CryoSPARC
      • CryoSPARC Cluster Integration Script Examples
      • Accessing the CryoSPARC User Interface
    • Deploying CryoSPARC on AWS
      • Performance Benchmarks
    • Using CryoSPARC with Cluster Management Software
    • Software Updates and Patches
    • Management and Monitoring
      • Environment variables
      • (Optional) Hosting CryoSPARC Through a Reverse Proxy
      • cryosparcm reference
      • cryosparcm cli reference
      • cryosparcw reference
    • Software System Guides
      • Guide: Updating to CryoSPARC v4
      • Guide: Installation Testing with cryosparcm test
      • Guide: Verify CryoSPARC Installation with the Extensive Validation Job (v4.3+)
      • Guide: Verify CryoSPARC Installation with the Extensive Workflow (≤v4.2)
      • Guide: Performance Benchmarking (v4.3+)
      • Guide: Download Error Reports
      • Guide: Maintenance Mode and Configurable User Facing Messages
      • Guide: User Management
      • Guide: Multi-user Unix Permissions and Data Access Control
      • Guide: Lane Assignments and Restrictions
      • Guide: Queuing Directly to a GPU
      • Guide: Priority Job Queuing
      • Guide: Configuring Custom Variables for Cluster Job Submission Scripts
      • Guide: SSD Particle Caching in CryoSPARC
      • Guide: Data Management in CryoSPARC (v4.0+)
      • Guide: Data Cleanup (v4.3+)
      • Guide: Reduce Database Size (v4.3+)
      • Guide: Data Management in CryoSPARC (≤v3.3)
      • Guide: CryoSPARC Live Session Data Management
      • Guide: Manipulating .cs Files Created By CryoSPARC
      • Guide: Migrating your CryoSPARC Instance
      • Guide: EMDB-friendly XML file for FSC plots
    • Troubleshooting
  • Application Guide (v4.0+)
    • A Tour of the CryoSPARC Interface
    • Browsing the CryoSPARC Instance
    • Projects, Workspaces and Live Sessions
    • Jobs
    • Job Views: Cards, Tree, and Table
    • Creating and Running Jobs
    • Filters and Sorting
    • View Options
    • Tags
    • Flat vs Hierarchical Navigation
    • File Browser
    • Blueprints
    • Workflows
    • Inspecting Data
    • Managing Jobs
    • Interactive Jobs
    • Upload Local Files
    • Managing Data
    • Downloading and Exporting Data
    • Instance Management
    • Admin Panel
  • Cryo-EM Foundations
    • Image Formation
      • Contrast in Cryo-EM
      • Waves as Vectors
      • Aliasing
  • Processing Data in cryoSPARC
    • Get Started with CryoSPARC: Introductory Tutorial (v4.0+)
    • Tutorial Videos
    • All Job Types in CryoSPARC
      • Import
        • Job: Import Movies
        • Job: Import Micrographs
        • Job: Import Particle Stack
        • Job: Import 3D Volumes
        • Job: Import Templates
        • Job: Import Result Group
        • Job: Import Beam Shift
      • Motion Correction
        • Job: Patch Motion Correction
        • Job: Full-Frame Motion Correction
        • Job: Local Motion Correction
        • Job: MotionCor2 (Wrapper) (BETA)
        • Job: Reference Based Motion Correction (BETA)
      • CTF Estimation
        • Job: Patch CTF Estimation
        • Job: Patch CTF Extraction
        • Job: CTFFIND4 (Wrapper)
        • Job: Gctf (Wrapper) (Legacy)
      • Exposure Curation
        • Job: Micrograph Denoiser (BETA)
        • Interactive Job: Manually Curate Exposures
      • Particle Picking
        • Interactive Job: Manual Picker
        • Job: Blob Picker
        • Job: Template Picker
        • Job: Filament Tracer
        • Job: Blob Picker Tuner
        • Interactive Job: Inspect Particle Picks
        • Job: Create Templates
      • Extraction
        • Job: Extract from Micrographs
        • Job: Downsample Particles
        • Job: Restack Particles
      • Deep Picking
        • Guideline for Supervised Particle Picking using Deep Learning Models
        • Deep Network Particle Picker
          • T20S Proteasome: Deep Particle Picking Tutorial
          • Job: Deep Picker Train and Job: Deep Picker Inference
        • Topaz (Bepler, et al)
          • T20S Proteasome: Topaz Particle Picking Tutorial
          • T20S Proteasome: Topaz Micrograph Denoising Tutorial
          • Job: Topaz Train and Job: Topaz Cross Validation
          • Job: Topaz Extract
          • Job: Topaz Denoise
      • Particle Curation
        • Job: 2D Classification
        • Interactive Job: Select 2D Classes
        • Job: Reference Based Auto Select 2D (BETA)
        • Job: Reconstruct 2D Classes
        • Job: Rebalance 2D Classes (BETA)
        • Job: Class Probability Filter
        • Job: Rebalance Orientations
      • 3D Reconstruction
        • Job: Ab-Initio Reconstruction
      • 3D Refinement
        • Job: Homogeneous Refinement
        • Job: Heterogeneous Refinement
        • Job: Non-Uniform Refinement
        • Job: Homogeneous Reconstruction Only
        • Job: Heterogeneous Reconstruction Only
        • Job: Homogeneous Refinement (Legacy)
        • Job: Non-uniform Refinement (Legacy)
      • CTF Refinement
        • Job: Global CTF Refinement
        • Job: Local CTF Refinement
        • Job: Exposure Group Utilities
      • Conformational Variability
        • Job: 3D Variability
        • Job: 3D Variability Display
        • Job: 3D Classification
        • Job: Regroup 3D Classes
        • Job: Reference Based Auto Select 3D (BETA)
        • Job: 3D Flexible Refinement (3DFlex) (BETA)
      • Postprocessing
        • Job: Sharpening Tools
        • Job: DeepEMhancer (Wrapper)
        • Job: Validation (FSC)
        • Job: Local Resolution Estimation
        • Job: Local Filtering
        • Job: ResLog Analysis
        • Job: ThreeDFSC (Wrapper) (Legacy)
      • Local Refinement
        • Job: Local Refinement
        • Job: Particle Subtraction
        • Job: Local Refinement (Legacy)
      • Helical Reconstruction
        • Helical symmetry in CryoSPARC
        • Job: Helical Refinement
        • Job: Symmetry search utility
        • Job: Average Power Spectra
      • Utilities
        • Job: Exposure Sets Tool
        • Job: Exposure Tools
        • Job: Generate Micrograph Thumbnails
        • Job: Cache Particles on SSD
        • Job: Check for Corrupt Particles
        • Job: Particle Sets Tool
        • Job: Reassign Particles to Micrographs
        • Job: Remove Duplicate Particles
        • Job: Symmetry Expansion
        • Job: Volume Tools
        • Job: Volume Alignment Tools
        • Job: Align 3D maps
        • Job: Split Volumes Group
        • Job: Orientation Diagnostics
      • Simulations
        • Job: Simulate Data (GPU)
        • Job: Simulate Data (Legacy)
    • CryoSPARC Tools
    • Data Processing Tutorials
      • Case Study: End-to-end processing of an inactive GPCR (EMPIAR-10668)
      • Case Study: End-to-end processing of encapsulated ferritin (EMPIAR-10716)
      • Case Study: Exploratory data processing by Oliver Clarke
      • Case Study: DkTx-bound TRPV1 (EMPIAR-10059)
      • Tutorial: Tips for Membrane Protein Structures
      • Tutorial: Common CryoSPARC Plots
      • Tutorial: Negative Stain Data
      • Tutorial: Phase Plate Data
      • Tutorial: EER File Support
      • Tutorial: EPU AFIS Beam Shift Import
      • Tutorial: Patch Motion and Patch CTF
      • Tutorial: Float16 Support
      • Tutorial: Particle Picking Calibration
      • Tutorial: Blob Picker Tuner
      • Tutorial: Helical Processing using EMPIAR-10031 (MAVS)
      • Tutorial: Maximum Box Sizes for Refinement
      • Tutorial: CTF Refinement
      • Tutorial: Ewald Sphere Correction
      • Tutorial: Symmetry Relaxation
      • Tutorial: Orientation Diagnostics
      • Tutorial: BILD files in CryoSPARC v4.4+
      • Tutorial: Mask Creation
      • Case Study: Yeast U4/U6.U5 tri-snRNP
      • Tutorial: 3D Classification
      • Tutorial: 3D Variability Analysis (Part One)
      • Tutorial: 3D Variability Analysis (Part Two)
      • Tutorial: 3D Flexible Refinement
        • Installing 3DFlex Dependencies (v4.1–v4.3)
      • Tutorial: 3D Flex Mesh Preparation
    • Webinar Recordings
  • Real-time processing in cryoSPARC Live
    • About CryoSPARC Live
    • Prerequisites and Compute Resources Setup
    • How to Access cryoSPARC Live
    • UI Overview
    • New Live Session: Start to Finish Guide
    • CryoSPARC Live Tutorial Videos
    • Live Jobs and Session-Level Functions
    • Performance Metrics
    • Managing a CryoSPARC Live Session from the CLI
    • FAQs and Troubleshooting
  • Guides for ≤v3.3
    • ≤v3.3 User Interface Guide
      • Dashboard
      • Project and Workspace Management
      • Create and Build Jobs
      • Queue Job, Inspect Job and Other Job Actions
      • View and Download Results
      • Job Relationships
      • Resource Manager
      • User Management
    • Tutorial: Job Builder
    • Get Started with CryoSPARC: Introductory Tutorial (≤v3.3)
    • Tutorial: Manually Curate Exposures (≤v3.3)
  • Resources
    • Questions and Support
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On this page
  1. Cryo-EM Foundations

Image Formation

The pages in this section provide background on the physical processes that occur in the microscope to generate and detect an image.

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Last updated 3 months ago