holocontour 0.1.1

A minimalist toolkit for holographic plankton image segmentation

A minimalist tool for holographic plankton image segmentation.

HoloContour

This repository provides a pipeline for segmenting holographic particle images using a hybrid region-growing and contour refinement method. It integrates with the MorphoCut framework and exports outputs compatible with EcoTaxa.

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🚀 Features

• Contour-based object detection with:
  • Intensity filtering
  • Histogram matching (optional)
  • Region growing from intensity minima
• Optional plot saving of initial vs. refined masks
• Compatible with EcoTaxaWriter
• YAML-based configuration
• Safe fallback for empty masks

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⚙️ Usage

1. Install Dependencies

pip install -r requirements.txt

python main.py --config configs/sample_config.yaml --input path/to/your/data

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🖼 Example

The figure below shows an example of the pipeline's segmentation output:

• Red dashed: Initial region estimate
• Blue solid: Refined segmentation contour

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License

This project is licensed under the MIT License - see the LICENSE file for details.

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