myopari 0.1.3

User-Friendly AI Software for Automated Quantitative CMR Reporting on Low-Cost, Energy-Efficient Devices

myopari

myopari is a napari plugin for cardiac MRI segmentation and report generation. It provides an interactive widget to:

• select a 2D or 3D image layer,
• run ONNX-based segmentation,
• compute basic volumetric metrics,
• optionally enrich the report with an LLM rewrite,
• save a markdown report.

Main Features

• Napari dock widget for interactive segmentation
• Built-in segmentation models:
  • TIRAMISU_ACDC
  • TIRAMISU_EMIDEC
• Works with both 2D images and 3D volumes
• Optional myocardium-only segmentation mode
• Markdown report generation with:
  • per-class volumes (mL)
  • myocardium mass estimate (g)
  • optional external patient info files (.cfg, .txt, .md)
• Optional LLM-based report rewriting (via llama-cpp-python)

Installation with pip

pip install myopari

Quick Start in napari

1. Launch napari.
2. Load a cardiac image (2D or 3D).
3. Open the widget:
   • Plugins -> myopari -> myopari
4. In the widget:
   • Click Select image layer
   • Choose Edge device
   • Choose Segmentation model
   • (Optional) Enable Myocardium only
   • Click Segment
5. A labels layer is added with a name like:
   • segmentation_<input_layer_name>_<count>

Report Workflow

After segmentation:

1. (Optional) Click Choose patient info files and pick .cfg, .txt, or .md files.
2. (Optional) Enable Use LLM for report.
3. Click Create report.
4. Click Save report to .md to export.

Notes:

• The report includes per-label volumes in mL and myocardium mass estimate.
• If a logo asset exists in Resources, it is embedded in the report and copied next to the saved markdown file.

Troubleshooting

• Segmentation runtime/provider issues:
  • Check installed ONNX Runtime package (onnxruntime vs onnxruntime-gpu)
  • Ensure CUDA and driver versions match your onnxruntime-gpu build
• LLM report generation fails:
  • Install llama-cpp-python
  • Ensure internet access for first model download
  • Disable Use LLM for report to keep standard report generation

License

MIT. See LICENSE.