Hi, I’m working on 3D images of cells like this.
I also have hand-made 3D coordinates for each cell center (which is probably not the exact center).
My aim is, for each cell, to obtain a sphere which fit, more or less, the volume of the given cell, but being quite new to ImageJ library and image analysis in general, I can’t find a way to do that.
I’ve already made a script to extract cube volumes around each cell so that I can work locally on a 3D interval of the marked center.
I think I should correct the center of mass first to find the center of the sphere, but I don’t know how actually (maybe identifying the local max looking in the NearestNeighborhood).
Then I thought it would be sufficient to select a threshold based on some statistics of the cell cube and then increase the sphere radius iteratively until it finds the border of the cell.
Is this procedure even quite valid?
I’m not looking for a specific answer, instead I’d like to know which ImageJ and/or ImgLib2 tools I should study to get this task done since I’m just a bit familiar with IJ ImageStacks and similar, not much more and have difficulties finding the right documentation/references.
Thank you in advance!