Posted by
Michael Doube on
Dec 30, 2009; 7:49pm
URL: http://imagej.273.s1.nabble.com/3D-shape-descriptors-tp3689894p3689895.html
Hi all
In response to requests here and in the real world (if university counts
as the real world), I've made a few adaptations to the 3D Object Counter
so that it can do a few fancy new tricks:
1) Label particles a lot faster. Recursion in particle labelling is
reduced and multithreaded so that jobs on big stacks end before our
universe does.
2) Euler calculations for each particle, returning Euler characteristic,
number of cavities and holes per particle.
3) Surfaces and surface area estimates of each particle
4) Ellipsoid fitting, so that people can work out the
oblate/prolate/scalene/spheroidal nature of their particles
5) Moments of inertia and orientation of principal axes
6) Thickness of each particle
7) Display graphical results in a 3D Viewer window, where you can select
each numbered particle
8) Display numerical results in a Results table
All calculations are done in 3D, and voxel methods are used except for
surface area and ellipsoid fitting, which use the results of Bene's
surface mesher.
At the moment it works on binary stacks, and I've only tested it on the
images I have to hand, so your feedback would be very valuable.
The plugin is part of BoneJ, which is available here:
http://doube.org/bonej.htmlOnce installed, there is a new item in Plugins->Analyze->Particle Analyser.
Have a happy new year,
Michael
--
Dr Michael Doube BPhil BVSc PhD MRCVS
Research Associate
Department of Bioengineering
Imperial College London
South Kensington Campus
London SW7 2AZ
United Kingdom