holocontour 0.1.2

A minimalist toolkit for holographic plankton image segmentation

HoloContour

Holocontour is a small but capable toolkit that turns raw in‑line digital holograms into clean binary masks of planktonic particles. It couples intensity‑driven region growing with a contour‑refinement step, and wraps everything in a reproducible, YAML‑configurable pipeline built on top of MorphoCut. Outputs ship in an archive ready for direct upload to 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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🖼 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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