Pixel Classification GUI (using ImageJ and R in Bio7)

I finally finished a first version of a Supervised Classification GUI using ImageJ and R within Bio7:

At the moment it can be installed into Bio7 3.1 following the Github documentation (see video below).

I reused the ROI Manager for the creation of classes using the underscore notation.

The plugin can be compiled dynamically. I tried to simplify the Java source so that it can be
extended easily. Feedback and suggestions are welcome.

The executed simple R scripts (using a Random Forest example) can be adapted easily for training and classification using the R package universe.

A big thank you to @schmid to solve and fix a thread blocking RankFilters mystery.

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An update of the plugin is available which simplifies the classification process with new options for the class transfer. Now you can simply:

  1. Open an image in ImageJ
  2. Create the ROI selections in the ROI Manager (using an underscore to mark the class signatures or using optionally ROI groups (thanks to @LThomas in ImageJ available).
  3. Transfer the ROI data as a matrix to R (now the stack data is hidden)
  4. Train the selected data with R
  5. Classify and predict new data (selected images or optionally recursive directories) with R



Now a dynamic classification preview can be generated from a selection:

I also added some easy R examples using different R packages (simply change the path to the scripts):

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