A paper describing our SlideJ plugin for processing digital slides using ImageJ has been published on PLOS ONE:

Della Mea V, Baroni GL, Pilutti D, Di Loreto C (2017) SlideJ: An ImageJ plugin for automated processing of whole slide images. PLoS ONE 12(7): e0180540.

The work was partially supported and funded by the EU FP7 program, AIDPATH project, grant number 612471.