Voxels Coordinates Particle Anlayiser - BoneJ


I have been sucessfully using the “Particle Analyzer” plugin from BoneJ for some time. Now I would like to perform some extra analysis of the particles and I would like to know the coordinates of the voxels forming every single particle so that I can then export this information to python for example and use some functions that I already have.

Does anybody know if we can export a file containing the voxels coordinates for every particle detected by such Plugin? If not, how could I access this information?

Thank you!

If you have a decent number of particles, your output file is going to be huge, especially if you encode coordinates in ASCII characters rather than int.

You may be better off accessing from your Python script the int[][] particle label image which is returned by ConnectedComponents.run() (or just save the float[][] display version interactively from ImageJ and then open in Python). That image contains all the info you need for the next step. It is all the particle labels (pixel values) arranged in coordinates (pixel locations) so all you have to do is for each particle label make a list of all coordinates of pixels with that label.