I would like to use the imagej-op fill holes as it can work also on a virtual images.
If you start from a binarized image (loaded as UnsignedByteType) one needs to convert it to to a BooleanType in order to pass it to fillHoles. I call again “threshold.apply” but I am sure there are easy ways to do it.
The behavior with a stack is puzzling. I would like to do a 2D fill holes for the whole XYZT stack. Currently it does not seem to fill any holes (it works if I pass a single plane). Does the fillholes apply the operation in 3D by default? If yes how to pass a 2D structuring element? Could you give an example for it or add such an example to the Jupyter notebook (https://nbviewer.jupyter.org/github/imagej/tutorials/blob/master/notebooks/1-Using-ImageJ/Ops/morphology/fillHoles.ipynb) ?
You can find the image at https://owncloud.gwdg.de/index.php/s/hj2ABIrgolWe3Xd t=1 Z_plane= 18