Plugin announcement: Orientation measurements

Posted by Per Christian Henden on Dec 05, 2007; 10:46pm
URL: http://imagej.273.s1.nabble.com/Plugin-announcement-Orientation-measurements-tp3697674.html

I've created a plugin for measuring the orientation of shapes in an image or stack using statistical calculations. I don't think there is such a plugin already.

Get it at http://www.pvv.org/~perchrh/imagej/orientation.html
The plugin is in the public domain (free license).

Theory of operation:

Requires a segmented input image or stack.
Calculates the orientation of all labels (intensity values) in the image by finding the eigenvector associated with the largest eigenvalue of the covariance matrix of the x,y,z coordinates of each label. For the mathematical details, see this [1] paper, pages 31-32 (23-24).

Jama (Java matrix package, public domain) is used for extracting the eigenvalues and eigenvectors from the covariance matrix. The vectors are normalized before printed.

The coordinate system of the image is used. That means (x=0,y=0) is at the topmost left corner of the screen. X-coordinates increase towards the right and y-coordinates increase downwards. Z-coordinates increase into the screen.

The image is read only once. The complexity of the algorithm is O(N), where N is the number of pixels in the image.

[1] http://www.pvv.org/~perchrh/papers/mastersthesisHendenBacheWiig.pdf

Cheers,

PER