Thanks for the help. I don’t have a script using XitoSBML at the moment as I am just trying to figure out what all things I can do using pyimagej and XitoSBML. Majority of the functions I have tried to call from python have thrown the Headless Exception.
Create_Img.run("run Spatial Image SBML Plugin")
>jnius.JavaException: JVM exception occurred: java.awt.HeadlessException
I am only able to run
Spatial_Img_SBML = autoclass('jp.ac.keio.bio.fun.xitosbml.Spatial_Img_SBML')
sbml = Spatial_Img_SBML()
>XitoSBML 1.2.0: Spatial SBML Plugin for ImageJ
Copyright (C) 2014-2019 Funahashi Lab. Keio University.
XitoSBML is an ImageJ plugin which creates Spatial SBML model
from segmented images. XitoSBML is not just a converter,
but also a spatial model editor so that users can add
molecules(species), reactions and advection/diffusion coefficients
to the converted Spatial SBML model.
More information is available at
So, I thought that I should try to access the inner level functions where some image processing is taking place but those functions have an ImagePlus object and some hash sets as their parameters and I am not so sure on how to get those.
Also, recording macros only gives this output and Im not sure what I can do with this.
run("run Spatial Image SBML Plugin", "save=C:/Users/Bhavay/Desktop/XitoSBML/examples/2D/abcd.xml");