KNIME - Read H5 files


I have a large dataset of H5 files made by Ilastik. Is it possible to open them in KNIME without previously converting them to tiff in FIJI ?
I’m a new KNIME user and I can’t find how to do it


Thanks a lot

Hi @LPUoO,

Currently, this would be the only way to load them into KNIME. You could, however, try to use our ilastik integration to execute your ilastik workflow directly from within KNIME. There are some pitfalls with this approach, though, in particular with respect to the structure of your input data. Also, which ilastik workflow has produced the H5 files?


Hi @stelfrich,
Thanks for the reply. I used the pixel + object classification from Ilastik. My plan was to measure 3D volumes and morphology of the objects then make Principal Component Analysis in KNIME and then with HiLite see the original 3D objects in different populations from the PCA.

But I’m thinking that probably the easiest is to measure 3D volumes and morphology in FIJI and once I have all the results make only the PCA and HiLite in KNIME.