HDF5 is a format that allows ilastik efficient block-wise processing of data. You will get the best performance in ilastik using this format. While the conversion to HDF5 is beneficial for any large dataset, we especially recommend it for multipage tiffs.
All features the plugin provides can be automated via Fiji macros (see our examples.)
In FIJI, go to Help->Update… In the dialog that appears, click the “Manage update sites” button. In the list of update sites, select “ilastik”.
You should now see
ilastik4ij.jar in your updater window.
After restarting Fiji you should see an ilastik entry in the Plugins menu:
Please visit the plugin documentation if you want to know more about the plugin usage.