User Guide

Get Started

• Installation
  • Prerequisites
  • Installation
  • Optional Dependencies
    • DTS Simulations
    • DTS Backmapping
  • Instructions for Developers
  • Getting Help
• Quickstart
  • Launch Mosaic
  • Loading Data
  • Basic Navigation
  • Save a Screenshot
  • Save a Session
  • Next Steps
• Concepts
  • UI Layout
  • Object Browser
  • Context Menu
  • Status Bar
    • Interaction Mode
    • Interaction Target
    • Processing Indicator
  • Coordinate System
  • Next Steps

Working with Data

• Import and Export
  • Import
  • Visual Properties
  • Screenshots
  • Animations
  • Export
  • Programmatic Access for Developers
  • Next Steps
• Session Management
  • Saving Sessions
  • Loading Sessions
  • Programmatic Access for Developers
  • Next Steps
• Specialized Views
  • Volumes
  • Trajectories

Feature Tabs

• Segmentation
  • Merge
  • Remove
  • Select by Size
  • Transform
  • Crop
  • Cluster
  • Outlier Removal
  • Normals
  • Trim
  • Skeletonize
  • Downsample
  • Properties
• Parametrization
  • Parametric Fitting
    • Sphere
    • Ellipsoid
    • Cylinder
  • Non-Parametric Fitting
    • RBF (Radial Basis Function)
    • Mesh
    • Curve
  • Sampling Operations
    • Sample
  • Mesh Operations
    • Repair
      • Remesh
    • Smooth
    • Project
    • Next Steps
• Intelligence
  • Equilibrate
  • HMFF
  • Trajectory
  • Backmapping
  • Detection
    • Template Match
    • Membrane

Practical Workflows

• Working with in situ data
  • Segmentation
  • Connected Components
  • Refinement
  • Clustering
    • Envelope Extraction
    • Leiden Clustering
  • Meshing
• Influenza A Virus
  • Requirements
  • Visual Demonstration
  • Membrane Segmentation
  • Mesh Creation
    • Clean the Segmentation
    • Generate Initial Mesh
    • Refine the Mesh
    • Equilibrate the Mesh
  • HMFF Simulation
  • Constrained Template Matching
    • Generate Seed Points
    • Template Matching
    • Refine Protein Picks
  • Coarse-Grained Martini Models
    • Backmapping
    • Coarse Graining
    • Equilibration
  • Conclusion
  • References
• Batch Processing
  • Requirements
  • Creating a Processing Pipeline
    • Configuring Input Files
    • Understanding the Processing Steps
    • Execution Settings
  • Running the Pipeline
    • Cluster Execution
  • Reviewing Results
  • Using Seed Points for Template Matching
  • Pipeline Operations Reference
    • Input
    • Preprocessing
    • Parametrization
    • Export
  • Troubleshooting

Reference

• File Formats
  • Volume Formats
    • MRC (.mrc, .map)
    • EM (.em)
    • HDF5 (.h5)
  • Point Cloud Formats
    • CSV (.csv, .xyz)
    • TSV (.tsv)
    • PDB (.pdb)
    • GRO (.gro)
    • STAR (.star)
    • CIF (.cif)
  • Mesh Formats
    • OBJ (.obj)
    • PLY (.ply)
    • STL (.stl)
  • Trajectory Formats
    • TSI (.tsi, .q)
    • VTU (.vtu)
  • Session Format
    • Pickle (.pickle)
  • See Also
• Troubleshooting
  • File Import Errors
  • Performance Issues
  • Selection Problems
  • Crashes During Operations
  • Export Failures
  • Missing Features in Exported Files
  • Session Won’t Load
  • Mesh Generation Failures
• Issues

Further Information

• License