I am using an automated pipeline combining cellprofiler .cppipe and ilastik .ilp files. The output from cellprofiler is a 6-channel 16bit composite image in h5 format, and I put this into an ilastik autocontext workflow that I have pretrained. Batch processing using this works smoothly on the local GUI version of ilastik1.3.3b1-OSX, but when I try to run this using headless mode using ilastik docker container (1.3.3post2) it fails and shoots up an AssertionError.
See above dropbox link to a folder where I have included the command used, error message, ilastik .ilp file and the .h5 input file to reproduce this error.
I would really appreciate any advice with this!