Exporting probability masks for more than 3 labels from ilastik

Hi all,

I’ve been trying to export probability_masks in .tiff format from ilastik with 4 labels. With only 3 labels, it works just fine and I can use them for further analysis in cellprofiler. However, exporting probabilities for 4 labels doesn’t work at all and when opening the .tiff files in fiji /imagej, they only show 3 channels that are more or less empty.

Is there a way to export probability masks for more than 3 channels?


Hi @cordel,

the tiff-writing abilities of ilastik are somewhat limited, that’s why we usually suggest to export to hdf5 and open the result in Fiji using the ilastik import/export plugin. Furthermore I would suggest converting the datatype to uint8 and renormalizing from [0.0, 1.0] to [0, 255] in the export dialog (resulting files are 4x smaller without loss of accuracy).