Particle Analyser

3D Particles This plugin performs connected-components labelling. It started life as an adaptation of the 3D Object Counter, for identifying particles as part of Purify. Once it became obvious that the heavily recursive algorithm was very inefficient, especially on large stacks, particle labelling was rewritten to be multithreaded and much less recursive. A further, single-threaded, non-recursive (runs in O(n) time) algorithm is available but is very heavy on RAM and only significantly outperforms the multithreaded algorithm on very large stacks, but can be faster on small stacks in some cases.

Since BoneJ v1.3.10, Particle Analyser joins particles using a 3-pass non-recursive approach that maps neighbourhoods as in a graph and merges them very quickly and memory-efficiently. This fast labelling feature is now the default method. It is listed as 'Mapped' in the algorithm selection drop-down.

Major speed improvements (50×) have been made to this plugin, available only in BoneJ2. For more details, see the preprint describing the new approach.

A member of our group wished to study osteocyte lacunae in synchrotron microCT images, so the Particle Analyser was born from Purify's particle labelling algorithm. Other groups use Particle Analyser for soil analysis; it could be used for any porous media. Particle Analyser labels unique (unconnected) particles, then analyses each particle separately. Substantial use is made of other plugins in BoneJ, including Connectivity to get the Euler characteristic, Isosurface to get the surface area and Thickness to get the local thickness of individual particles.

Installs in the ImageJ menus under Plugins->Analyze->Particle Analyser.

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