ImgLib2 Mesh

3D triangle mesh data structures and algorithms for ImgLib2.

ImgLib2 Mesh provides a lightweight Mesh interface, several implementations, and a collection of algorithms for building meshes from images, measuring them, transforming them, and turning them back into images.

Features

Data structures

• Mesh — a collection of Vertices (position, normal, texture coordinates) and Triangles (vertex indices plus a normal), with coordinates accessible as float or double.
• BufferMesh — backed by java.nio buffers, suitable for handing off to OpenGL-style renderers.
• NaiveFloatMesh / NaiveDoubleMesh — simple growable array-backed meshes.
• TranslateMesh and ReadOnlyMesh — lightweight views over an existing mesh.

Algorithms (mostly exposed via Meshes and MeshStats)

Task	Classes
Image → mesh	Marching cubes for BooleanType and RealType images
Mesh → image	EuclideanDistanceVoxelization (and the deprecated Voxelization)
Cleanup	RemoveDuplicateVertices, SimplifyMesh, TaubinSmoothing, normal calculation
Topology	MeshConnectedComponents, Meshes.merge
Geometry	Convex hull (quickhull), ellipsoid fitting, inertia tensor, bounding box, centroid
Shape descriptors	Volume, surface area, solidity, convexity, sphericity, compactness, elongation, …
Queries	Point-in-mesh tests (Interior), ray–triangle intersection (MollerTrumbore)
Slicing	ZSlicer — cut a two-manifold mesh with Z planes into closed contours
Transforms	Translate, scale

I/O (net.imglib2.mesh.io)

• PLYMeshIO — read and write PLY (ASCII and binary).
• STLMeshIO — read and write binary STL.
• XYZPointsIO — read XYZ point clouds.

Many algorithms are also annotated for discovery by SciJava Ops (e.g. geom.size, geom.boundingBox), so they can also be called as ops.

Installation

ImgLib2 Mesh is released to the SciJava Maven repository. Add the repository and dependency to your pom.xml:

<repositories>
	<repository>
		<id>scijava.public</id>
		<url>https://maven.scijava.org/content/groups/public</url>
	</repository>
</repositories>

<dependencies>
	<dependency>
		<groupId>net.imglib2</groupId>
		<artifactId>imglib2-mesh</artifactId>
		<version>1.2.0</version>
	</dependency>
</dependencies>

If your project extends pom-scijava, the version is managed for you and can be omitted.

Usage

See ExamplesTest.java for worked examples: building a mesh from an image and measuring it, building one by hand, reading and writing files, and a tour of other operations. They run as part of the test suite, so they stay in sync with the API. The other unit tests show more usage.

Building from source

Building requires JDK 11.0.17 or newer and Maven; the resulting library targets Java 8.

git clone https://github.com/imglib/imglib2-mesh
cd imglib2-mesh
mvn clean install

Contributing

Bug reports and pull requests are welcome on GitHub. For questions and discussion, visit the Image.sc Forum.

License

ImgLib2 Mesh is distributed under the Simplified BSD License.