ilastik Fiji plugin

This plugin allows you integrate ilastik with Fiji. The main functionality of the plugin is import and export to HDF5 format and running trained ilastik workflows from within Fiji.

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.

ilastik workflows currently supported by the plugin are Pixel Classification, Autocontext, Object Classification, Multicut, and Tracking Workflows.

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.