Frangi Vesselness Filter
Detects tubular structures using the Hessian matrix eigenvalues at multiple scales (sigmas). Outputs a probability map where bright = vessel-like. Only sigmas above the selected threshold are used, so higher sigma = only thick vessels detected.
✏ Draw ROI (Region of Interest)
Click to place polygon vertices on the vesselness map. Double-click or snap to the first point to close. Only pixels inside the ROI contribute to the vessel area calculation. Use Copy ROI / Paste ROI to apply the same region across multiple images.
🖌 Paint Tool
Manually mark vessel gaps that the filter missed. Strokes are stored in image coordinates and added to the vessel binary mask when ▶ Run is clicked. Five brush sizes available. Use 🧹 Erase to remove individual strokes.
🎬 Sequence Analysis
For cardiac cycle image stacks. Select frames → compute a projection (Mean/Median/Min/Max Vesselness/Std Dev) → Auto-Optimize min segment size on the projection → Apply Projection Template to all frames → Analyze all frames in batch.
Auto-Optimize
Tests all min segment sizes on the projection image and finds the "elbow" — the point where increasing min size stops removing noise and starts removing real vessels. The bar chart visualizes this transition.
Projection-Guided Fill
For cardiac sequences: where the max vesselness projection detects a vessel (across all frames) AND the current frame has any vesselness signal there (even weak), the threshold is relaxed. Controlled by the Guide Strength slider (0–100%).
📐 Projection Template
Harder version of guided fill. Builds a binary vessel mask from the projection and overlays it as a cyan region on every frame. When ▶ Run is pressed, the template forces vessel detection at 25% of the normal threshold inside template regions.
🔢 Count Vessels
Manually count vessels by clicking on the overlay image. Each click places a numbered yellow marker. Click an existing marker to remove it (remaining markers renumber automatically). When you click Stop Count, the Width tool activates automatically if markers exist. Press ESC at any time to exit.
📏 Width Measurement
Draw a measurement line across a vessel: click to set the start point, then click to set the end point. The pixel distance and µm distance (using the current µm/px setting) are displayed on the line. If vessel count markers are present, the measurement is automatically linked to the nearest marker (within 80 image pixels). Multiple lines can be drawn per frame. Open 📋 Width Log to see a summary table with mean and SD per vessel, and to export to CSV. Press ESC to cancel a pending start point.