I am beginner in Ilastik and Knime, so maybe this issue has been solved somewhere.
My current “non-Knime” worflow is : generate images (tif) of cells from my experiment, segment the cells with Ilastik (pixel classification), process the hdf5 files from Ilastik with a homemade jupyter script to fit the shape of the cells with an ellipse.
I would like to automatize image processing with Ilastik. So, Knime seems adapted to me (actually I already tried the Ilastik plugin for Fiji but it was too long).
Thanks to example workflow available on Ilastik integration page (https://www.knime.com/book/ilastik-integration), I have been able to run somes images of my experiment.
The result can sucessfully be seen in Image normalizer node.
However, in Knime, when I put the “Jupyter” node after the “Ilastik” node, my Jupyter script is not working.
I have the feeling that is because, in Knime, “Ilastik” outputs are dataframes and not hdf5 files.
Is that so ? And if it is, how to deal with this issue ?
Thanks you very much for your help !
Kindly yours !