To cite Icy:
de Chaumont, F. et al. (2012)
Icy: an open bioimage informatics platform for extended reproducible research, Nature Methods, 9, pp. 690-696
https://icy.bioimageanalysis.org
Please mention the version of Icy you used (bottom right corner of the GUI or first lines of the Output tab.
To cite a plugin: go to the documentation page of the plugin (search the plugin name in the search bar of Icy and left click on it, or search directly on the Icy website) and look if there is a citation at the top of the documentation.If there is none, please contact the authors of the plugin to see how to cite it. Worse case, give at least its name, its version and a link to its documentation on the Icy website.
To cite a protocol: same as for plugin.