OCToolkit: General OCT Acquisition & Analysis Toolkit

Welcome to OCToolkit, a versatile, modular toolkit for retinal OCT and OCT-A data acquisition, conversion, and analysis.

Overview

OCToolkit provides:

• Data Ingestion: Support for HEYEX .e2e files, .fds, and other vendor formats
• Conversion Modules: Export to DICOM (slices, fundus, multi-frame volumes) and common image formats
• Analysis Pipelines: Segmentation, thickness mapping, layer quantification, OCT-A flow metrics
• Visualization Tools: Interactive B-scan viewers, en-face projections, 3D volume rendering
• Batch Processing: Command-line tools and scripts for large-scale studies
• Extensibility: Easily add new file readers, analysis modules, or export formats

Project Structure

OCToolkit/
├─ README.md                # This overview
├─ conversion/              # .e2e → DICOM conversion programs
│  ├─ README.md             # Specific conversion instructions
│  └─ e2e_to_dcm.py         # Conversion script
├─ segmentation/            # OCT layer segmentation modules
├─ metrics/                 # Quantification pipelines (thickness, OCT-A flow)
├─ visualization/           # B-scan and volume viewers
└─ utils/                   # Utility functions (I/O, metadata handling)

Installation

conda create -n octoolkit python=3.11 pip -y
conda activate octoolkit
pip install oct_converter pydicom numpy pillow
# add other dependencies for segmentation, visualization as needed

Getting Started

1. Convert your raw .e2e scans: see conversion/README.md.
2. Segment layers: modules under segmentation/.
3. Compute metrics: scripts in metrics/.
4. Visualize results: launch tools in visualization/.

Contributing

• Fork the repo and submit pull requests.
• Add new readers under conversion/ or modules under segmentation/, metrics/, etc.
• Ensure code passes tests and includes documentation.

License

Distributed under the MIT License. See LICENSE for details.