Thanks @mdoube, I was not aware that there was such a big performance improvement with the Particle Analyser under Bone J2. Last time I tried it (about a year ago I think), the Particle Analyser was under the Legacy section of the code, so I got the impression that it was unchanged from Bone J1.
I did once compare the Particle Analyser of Bone J1 to Object_Counter3D by Fabrice P Cordelires and found BoneJ 1’s version to be much faster. I also compared BoneJ particle analyser to Avizo and found Avizo to be much faster. But I see from your recent paper that you now have revised the algorithm so that it matches Avizo, that is interesting. Thanks for this info.