napari-myelin-quantifier 0.3.1

Myelinated Axon Quantification with Label Tracking

napari-myelin-quantifier

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Overview

napari-myelin-quantifier is a napari plugin for quantitative analysis of 2D cross-sectional myelinated axons from binary segmentation masks.

The plugin identifies individual myelin rings, assigns a unique ring_id to each structure, and exports morphometric measurements for downstream analysis.

It enables reproducible extraction of:

• Axon diameter
• Fiber diameter
• Myelin thickness
• g-ratio

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Installation

Install via pip:

pip install napari-myelin-quantifier

If napari is not installed:

pip install "napari-myelin-quantifier[all]"

Development version:

pip install git+https://github.com/wulinteousa2-hash/napari-myelin-quantifier.git

Input Requirements

The plugin requires a binary mask layer:

• Myelin = foreground (1 / True)
• Background = 0 / False
• Recommended: clean segmentation without holes or broken rings

Example Binary Mask

Ring Detection and Labeling

Each connected myelin ring is:

• Assigned a unique ring_id

• Spatially localized using centroid coordinates

• Evaluated for ring topology using Euler characteristic

Example Labeled Output

Topological Validation (Euler Characteristic)

The Euler number ensures valid ring topology:

• Euler = 0 → valid ring (one hole)

• Euler ≠ 0 → solid object or fragmented structure

This prevents non-myelinated artifacts from being included in analysis.

Topology Illustration

Quantitative Output (CSV)

For each ring, the plugin exports:

ring_id

centroid_x, centroid_y

bbox_x0, bbox_y0, bbox_x1, bbox_y1

ring_area_px

lumen_area_px

filled_area_px

euler

touches_border

Example:

ring_id,centroid_x,centroid_y,bbox_x0,bbox_y0,bbox_x1,bbox_y1,ring_area_px,lumen_area_px,filled_area_px,euler,touches_border
1,873.8658,34.4421,857,18,890,52,380,556,936,0,False

Derived Morphometric Parameters

Assuming approximately circular cross-sections:

Axon diameter:

d_axon = 2 × sqrt(lumen_area / π)

Fiber diameter:

d_fiber = 2 × sqrt(filled_area / π)

Myelin thickness:

t = (d_fiber − d_axon) / 2

g-ratio:

g = d_axon / d_fiber

Note: These are geometric approximations. For highly irregular axons, area-based statistics may be preferable.

Typical Workflow

1. Load binary mask into napari.

2. Open:

• Plugins → Myelin Quantifier

3. Adjust filtering parameters:

• Minimum ring area

• Minimum lumen area

• Exclude border objects (recommended)

4. Run quantification.

5. Export CSV.

6. Perform statistical analysis in Python, R, or Excel.

Interface

Contributing

Contributions are welcome. Please ensure tests pass before submitting pull requests.

License

MIT License.