I have a lot of ilastik .h5 probability images that I wish to batch post process in FIJI.
Importing ilastik HDF5 images works fine via Plugins > ilastik > Import HDF5 . In my case the dimensions are already correct as the default setting xyzc and I can successfully load the image by clicking “Load Raw”.
This command is macro recordable and I get the IJ-macro:
run("Import HDF5", "hdf5filename=path\\to\\my\\image_Probabilities.h5");
However, when I run this macro command it does not open the image but the dimensions selection splash screen instead.
Is there a way to include my dimension selection and “load raw” in the macro/script?
It does not have to be a IJ-macro, it could also be jython or groovy.
edit: tagging in @wolny as the maintainer of the plugins update site.