//load ImageJ
%classpath config resolver scijava.public https://maven.scijava.org/content/groups/public
%classpath add mvn net.imagej imagej 2.0.0-rc-67

//create ImageJ object
ij = new net.imagej.ImageJ()

ij.op().help("filter.min")

input = ij.scifio().datasetIO().open("http://imagej.net/images/clown.jpg")

//grab the first slice (index 0) from the channel dimension (index 2)
imageToFilter = ij.op().run("hyperSliceView", input, 2, 0)

ij.notebook().display(imageToFilter)

import net.imglib2.algorithm.neighborhood.HyperSphereShape

radius = 3 as int
shape = new HyperSphereShape(radius)

output = ij.op().run("create.img", imageToFilter)
ij.op().filter().min(output, imageToFilter, shape)

ij.notebook().display(output)