TomoGUI
User Guide
Installation
Requirements
Python Version
Core Dependencies
External Tools
AI Reco
Installation Methods
From Source (recommended)
Using Conda Environment
Verifying Installation
Troubleshooting
Qt Platform Plugin Issues
PyQt5 Import Errors
CUDA Issues
AI Reco model not found
Getting Started
Launching TomoGUI
Basic Workflow
Your First Reconstruction
Understanding the Interface
Main Layout
Log Output
Next Steps
Interface Overview
Main Window Layout
Top tab bar
Left Panel
Data Selection
Tab System
Main Tab
Reconstruction Parameters Tabs
Advanced Config Tab
Batch table (on the Main tab)
HDF5 Viewer
Right Panel
Image display
Log Output
Reconstruction Workflow
Quick reference
Try vs Full
Try Reconstruction
Full Reconstruction
Reconstruction Methods
Centre of Rotation
Output folders
Per-dataset parameters
AI Reconstruction
How it works
Single-file AI Reco
Batch AI Reco
Fix COR Outliers
Algorithm
Series tinting and auto-skip
TomoLog auto-contrast
Batch Processing Guide
Overview
Quick start
Per-file and top-bar COR
Series-aware operations
Series grouping
Series tinting
Auto-skip undersized files
Fix COR Outliers (also fills missing CORs)
Deleting files from the list
Remote / multi-GPU
Themes
Toggling
Customising
Features
Main Tab
Layout
Reconstruction parameter tabs
Right-hand visualisation
Auto-contrast
Log output
Reconstruction Parameters
Recon tab
Hardening tab
Phase tab
Rings tab
Geometry tab
Data tab
Performance tab
Per-dataset persistence
Batch Processing Tab
Features
File table
Selection
Batch Try / Full
Batch AI Reco
Fix COR Outliers (also fills missing CORs)
Auto-skip undersized files
Delete Selected
Remote execution
HDF5 Data Viewer
Opening a file
Image tab
Metadata tab
Expected structure
Common failures
See Also
Advanced Configuration
Fields
Persistence
Config file editing
TomoLog Integration
Launching TomoLog
Dialog fields
Per-file auto-contrast
Advanced Topics
SSH Setup for Remote Machines
Requirements
Configuring TomoGUI
Non-interactive shell env
Shared storage
Troubleshooting
GPU Management
Single-file mode
Batch mode (unified queue)
Per-phase subprocesses
Monitoring
Remote GPUs
COR Management
Sources of COR
Resolution order (batch)
Storage
Fix COR Outliers
Why series grouping?
Auto-skip undersized files
Troubleshooting
GUI / launch
Reconstruction
AI Reco
TomoLog
Developer Guide
Architecture
Packages
Layering
Key subsystems
Unified batch queue
AI Reco pipeline
Fix COR Outliers
Per-dataset parameter persistence
API Reference
Main classes
Entry points
Inference pipeline
Internal helpers (TomoGUI methods)
Contributing
Development Setup
Code Style
Testing
TomoGUI
Index
Index