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After 3 years of macro development during my PhD, I've taken the natural step onwards into Java plugin development. These plugins are provided as-is: I write them to be useful, but if you find that they don't work as you think they should then please email me.
Rotating Calipers calculates the minimum and maximum diameters of an ROI as they would be measured with real, parallel callipers. The method is adapted from this description. It is a port from this macro.
Align 3D takes a 16-bit stack of CT images, calculates moments of inertia and aligns the image content to the principal axes, and draws the axes on the stack for visualisation with the ImageJ 3D Viewer. It assumes images of bones in air, so the default threshold and density values are set accordingly. Nearest neighbour interpolation is used. Thanks to Stephan Saalfeld for useful comments. You will need to install the JAMA matrix mathematics package in order to compile and run Align 3D.
Fit Sphere takes a set of point ROIs from the ROI manager and calculates a best fit sphere using an iterative algorithm. Ported from Angelo Tardugno's C++. You will need the JAMA jar file in your ImageJ plugins directory to run this plugin.
Volume Fraction measures the proportion of an ROI that is thresholded. It works for stacks, calculating the volume fraction limited by the threshold, the top and bottom slices specified and the ROI. Thanks to Wayne Rasband for pointing out the bleeding obvious.
This file last modified 0013hrs 17 November 2008 © Michael Doube 2004-2008 :: Designed to be interoperable and standards-compliant. Looks best with Mozilla Firefox