Import Multiple Models from Ilastik


I’ have many images (100+) segmented in Ilastik. I want to use them to build Deep Learning Segmentation models in MIB. I have been able to import these one at a time, but cannot import multiple images plus their models at the same time.

If I have a image plus model opened in MIB and try to open a second image plus the model from an h5 file (output from ilastik) it replaces the previous model. I can’t find a way to quickly add images and their associated ilastik models all at once. Is there a trick to do this easily?


Hi Lee,
do you have images as individual 2D slices and h5 files as individual 2D slices?
The typical way of importing h5 files from ilastik is to load the images as stack and load corresponding model that is stored in a single h5 file.
Do you have a different setup?

Thanks for the tip. That will work. I had been using individual files in Ilastik. I will be sure to work with a stack instead and then it should go easily.