Import multichannel HDF5 into ilastik

Hi all, I hope the data treats you well.

Does anybody know if it’s possible to import multichannel HDF5 (.h5) files into ilastik? Is there a default way to name the data internally to lead ilastik to open as multichannel. I’ve tried:
and it opens a dialog for me to select one of the two options, e.g. /channel0, or /channel1

I’m wondering if it’s just single channels with this file type.


Hi @nranthony,

you can import such a multichannel image by using the stack import. So in the Data Selection applet you should choose Add new -> Add a single 3D/4D volume from sequence (coming to think of it the naming isn’t the best here…). This will open up a new dialog for you. There you select your h5 file. This will open up yet another dialog :slight_smile:. This is where you specify the internal datasets. Note that the placeholder ilastik uses is the *.
So for your case you could enter data/channel* in this dialog - there should also be a preview (in my case I had the internal path test/data-*).:


Note, that if you want to stack all datasets in your file a simple * will suffice as a pattern (given they have the same dimensionality, data type).

Once you are satisfied hit okay and make sure to select C as the stacking axis:


Side note: you could also directly specify the pattern without the additional dialog (and it is automatically generated for you, too, as you can see in the above screenshot).