@ukitel and @mlauber71 thanks for your input. Sorry for the late response, I was travelling.
I created a new workflow (created from scratch on a PC with czi images) and it worked regardless of the memory allocated to ilastik in the configuration panel. However, for the workflow shared by my colleague (created on a mac with a table created form czi images which works on the mac) and my old workflow (created on a PC -using the same nodes as the new one- with a tiff exported form a czi through QuPath and ImageJ, uploaded on message above on Mar 28) I still get the same error even when matching the memory allocated to ilastik in the configuration panel to that available on the task manager.
@mlauber71 The reason why it doesn’t work on the workflow created on the mac could be a path error not adapted to the OS environment, but I don’t know where to check/correct the path for the temporary files for knime/ilastik communications. The correct path for the temp file is D:\Users\zeiss\AppData\Local\Temp\ilastik not D:\Users\zeiss\AppData\Local\Temp/ilastik/f2c09662-e01d-43de-b5a5-feac0c17a63c/file0_result.tiff as stated in the error.
For the old workflow, I don’t know… It’s ok for now, I was able to solve that image cohort using another segmentation and I can work on my current cohort with ilastik, but the issue has not been fully resolved.
FYI @gab1one @christian.dietz @stelfrich