Modan2
Contents:
Installation
System Requirements
Installation Methods
Windows
macOS
Linux
Troubleshooting
Windows: missing DLL on startup
macOS: “Modan2 is damaged and can’t be opened”
Linux: “Could not load the Qt platform plugin xcb”
OpenGL / 3D Rendering Errors
Performance Issues
Verifying Installation
Updating Modan2
Updating from 0.2.0-beta.1 or earlier (Windows)
Uninstalling Modan2
Getting Help
Next Steps
Quick Start
1. Install
2. Create a dataset
3. Get your data in
4. Digitize landmarks
5. Add variables (optional)
6. Run the analysis
7. Explore the results
Typical workflow
Essential shortcuts
Quick fixes
Next steps
User Guide
Getting Started
Launching Modan2
Main Window Overview
Working with Datasets
Creating a New Dataset
Dataset Variables
Editing and Organising Datasets
Importing Data
Importing 2D Images
Importing 3D Models
Importing Landmark Files
Importing a Dataset Package (JSON+ZIP)
Working with Objects
Viewing an Object
Placing Landmarks (2D)
Placing Landmarks (3D)
Editing Landmark Coordinates
Missing Landmarks
Landmark Names
Semi-landmark Curves
Calibration (Setting the Scale)
Digitizing Aids
Display Options
Statistical Analysis
Overview
Running an Analysis
Procrustes Superimposition
Principal Component Analysis (PCA)
Canonical Variate Analysis (CVA)
MANOVA
Handling Missing Landmarks
Visualization
2D Viewer
3D Viewer
Statistical Plots
Data Export
Exporting Datasets
Exporting a Dataset Package (JSON+ZIP)
Exporting Analysis Results
Keyboard Shortcuts
Main Window
Object Dialog (Curve mode)
Preferences
General
Viewer Appearance
Plot Appearance
Tips and Best Practices
Data Organization
Landmark Placement
Statistical Analysis
Performance Optimization
Common Workflows
Workflow 1: 2D Morphometric Study
Workflow 2: 3D Morphometric Study
Workflow 3: Missing Data Study
Troubleshooting
Analysis Fails
Landmarks Not Showing
Slow Performance
File Format Reference
TPS
NTS
Morphologika
X1Y1
Glossary
Next Steps
Frequently Asked Questions (FAQ)
General Questions
What is Modan2?
Who is Modan2 for?
What makes Modan2 different from other morphometrics software?
What file formats does Modan2 support?
Installation and Setup
What are the system requirements?
How do I install Modan2?
Where is my data stored?
Can I keep my data somewhere else?
Can I backup my data?
Data Management
What is a dataset in Modan2?
How do parent-child datasets work?
What is the difference between objects and datasets?
How many landmarks can I use?
Can I have missing landmarks?
Can I capture curves instead of individual points?
Landmark Digitization
How do I digitize landmarks on 2D images?
How do I digitize landmarks on 3D models?
Can I edit existing landmarks?
Statistical Analysis
What analyses does Modan2 support?
How do I run an analysis?
What is Procrustes superimposition?
How many objects do I need for analysis?
File Import and Export
How do I import landmark data?
Can I import from other software?
How do I export my data?
What is JSON+ZIP export?
Performance and Optimization
How fast can Modan2 handle large datasets?
Can I improve performance?
What if analysis is taking too long?
Troubleshooting
Where do I get help?
How do I report a bug?
Why does Modan2 crash?
The 3D viewer is not working
Advanced Topics
Can I use Modan2 in a publication?
Can I extend Modan2 with custom analyses?
How does the database work?
Can I run Modan2 on a server?
Development and Contributing
Is Modan2 open source?
Can I contribute to Modan2?
What features are planned?
Who develops Modan2?
License and Legal
Can I use Modan2 commercially?
What if Modan2 damages my data?
Still Have Questions?
Troubleshooting Guide
Where Modan2 Keeps Your Files
Installation Issues
Application Will Not Start
Permission Issues
Database Issues
Database File Corrupted
Cannot Access Database
Data Loading and Import Issues
Import File Format Not Recognized
Missing Data After Import
Image/Model Not Loading
Analysis Errors
PCA/CVA/MANOVA Fails
Procrustes Alignment Issues
Analysis Results Look Wrong
3D Visualization Issues
3D Viewer Black Screen
OpenGL Errors
Landmark Spheres Not Visible
Performance Issues
Application Slow to Start
Slow Analysis or Visualization
Out of Memory Errors
UI and Display Issues
UI Elements Not Displaying Correctly
Font Issues
High DPI Display Issues
Advanced Troubleshooting
Collecting Debug Information
Enabling Debug Logging
Other Startup Options
Common Error Messages
“Failed to connect to database”
“Procrustes superimposition failed”
“Not enough objects for analysis”
“Invalid landmark count”
Getting Additional Help
Known Issues and Limitations
Current Limitations
Planned Improvements
Contributing
Advanced Features Guide
Performance Optimization
Database Optimization
Large Dataset Strategies
Performance Benchmarks
Advanced Data Management
Hierarchical Datasets
Batch Operations
Semi-landmark Curves at Scale
Database Direct Access
Advanced Statistical Analysis
Custom Analysis Workflows
Superimposition Methods
Missing Landmark Handling
3D Visualization Techniques
Advanced 3D Controls
Landmark Visualization
Model Import and Processing
Integration with External Tools
R Integration
Python/NumPy Integration
MorphoJ Compatibility
Scripting and Automation
Python API
Database Queries
Batch Export
Custom Visualizations
Matplotlib Integration
Shape Deformation Grids
Settings and Configuration
Preferences File Format
Command-Line Options
Tips and Tricks
Keyboard Shortcuts
Workflow Optimization
Hidden Features
Further Resources
Developer Guide
Project Overview
Architecture
High-Level Overview
Database Schema
MVC Pattern in Modan2
File Formats
Development Setup
Prerequisites
Cloning the Repository
System Dependencies (Linux)
Virtual Environment Setup
Running from Source
Development Dependencies
Code Quality Tools
Testing
Test Framework
Running Tests
Writing Tests
Code Style Guidelines
General Principles
Naming Conventions
Docstring Format
PyQt5 Patterns
Common Tasks
Adding a New Dialog
Adding a New Analysis Method
Adding a New File Format
Contributing
Git Workflow
Commit Message Guidelines
Pull Request Process
Code Review Checklist
Building Executables
PyInstaller Configuration
Platform-Specific Builds
InnoSetup Installer (Windows)
Creating Releases
Database Migrations
Creating a Migration
Running Migrations
Advanced Topics
Custom Widgets
Statistical Extensions
Plugin System (Future)
Profiling and Optimization
Debugging
Useful Commands
Resources
Documentation
Morphometric Analysis
Community
License
Changelog
[Unreleased]
Added
Fixed
Changed
[0.2.0-beta.2] - 2026-07-28
⚠️ Upgrading from 0.2.0-beta.1 or earlier (Windows)
Changed
Fixed
[0.2.0-beta.1] - 2026-07-27
Added
Fixed
Changed
Documentation
Internal
[0.2.0-alpha.2] - 2026-07-24
Fixed
Added
Changed / Internal
[0.2.0-alpha.1] - 2026-07-23
Added
Changed
[0.1.12] - 2026-07-21
Added
Changed
Fixed
[0.1.8] - 2026-07-21
Added
Changed
Fixed
[0.1.7] - 2026-07-21
Changed
Fixed
[0.1.6] - 2026-07-20
Added
Changed
Fixed
Technical
[0.1.5] - 2026-07-18
Added
Fixed
Changed
Technical
[0.1.5-beta.2] - 2025-11-03
Added
Changed
Fixed
Technical
[0.1.5-beta.1] - 2025-10-08
Added (Phase 7 - Performance Testing & Scalability)
Changed
Performance
Documentation
[0.1.5-alpha.1] - 2025-09-11
Added
Changed
Fixed
[0.1.4] - 2025-09-10
Added
Changed
Fixed
Removed
[0.1.3] - 2024-06-21
Added
[0.1.2] - 2024-05-30
Added
[0.1.1] - 2024-04-12
Added
[0.1.0] - 2024-03-01
Added
Modan2
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