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User Guide

Installation
Quick Start
Image Processing Parameters
Example data
Running Tests
Troubleshooting

Examples

1. Reconstructing photoacoustic data
2. Comparing image reconstruction methods
3: Command Line Usage
4: Time-Series MSOT Data Analysis
5: Writing your own reconstruction algorithm
6: Writing your own scan reader

Developers

File Format Specification
Contributing to PATATO

API Reference

Analysis Code
- patato
Convenience Scripts
- convenience_scripts
  - convert_binary_to_hdf5
    
    main
    
    strtobool
  - convert_simpa
    
    main
    
    strtobool
  - copy_rois
    
    init_argparse
    
    main
  - data_analysis
    
    analyse_dce
    
    analyse_gas_challenge
  - generate_core
    
    init_argparse
    
    main
  - import_clinical_data
    
    init_argparse
    
    main
  - import_ithera_recons
    
    init_argparse
    
    main
  - print_speeds
    
    init_argparse
    
    main
  - process_msot
    
    main
  - rename_scan
    
    init_argparse
    
    main
  - scan_status
    
    init_argparse
    
    main
  - split_rois
    
    init_argparse
    
    main
  - unmix
    
    init_argparse
    
    main
  - view
    
    init_argparse
    
    main
Useful Utilities
- useful_utilities

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By Thomas Else

© Copyright 2025, Thomas Else.