ijGeodesics is an open-source, Java-based plugin for the scientific image processing software ImageJ. Developed largely in conjunction with researchers at INRAE, it is designed to calculate distance functions and measure the geodesic properties of particles within binary 2D digital images. Core Functionalities
Unlike standard Euclidean geometry (which measures a straight line across a grid), a “geodesic path” in image processing refers to the shortest series of neighboring pixels connecting two points entirely within a specific particle’s shape. ijGeodesics delivers two primary calculations:
Geodesic Diameter: Computes the length of the longest possible geodesic path entirely contained inside a particle. This is highly useful for irregular or curved shapes where a standard bounding box or ferret diameter would include empty spaces outside the particle.
Chamfer Distance Propagation: Calculates and propagates distances from a specific starter binary image (the marker) while being physically constrained to the bounds of a second binary image (the mask). Extracted Parameters
When run on a label image, the plugin extracts several parameters for each distinct particle: Geodesic Diameter: The maximum shortest-path length.
Radius: The radius of the greatest enclosed circle that can fit inside the particle.
Geodesic Elongation: The ratio of the geodesic length over the inscribed circle’s radius, signaling how “stretched” or winding a particle is.
Extremity Coordinates: The physical (x,y) coordinates mapping out the exact furthest points of the detected geodesic path. How to Install and Use It
Download: Obtain the compiled package file, typically named ij_Geodesics.jar.
Install: Drag or copy the .jar file directly into the plugins subfolder of your local ImageJ installation directory.
Run: Restart ImageJ, open your binary or labeled threshold image, and locate the tool under the Plugins drop-down menu.
Visualize: If you select the “Overlay results” checkbox in the plugin window, ImageJ will visually draw the geodesic line and the inscribed circle directly over your particles for rapid verification. Parallel Alternatives
If you prefer working in a Python or MATLAB ecosystem instead of Java/ImageJ, the same algorithm logic is packaged by the authors as imGeodesics, which functions as a native library for MATLAB.
Are you planning to use ijGeodesics for a specific project, such as analyzing cell biology structures, material composites, or food science textures? Let me know your use case, and I can give you more specific advice on setting up your image masks. Chamfer distances and Geodesic diameters
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