QuPath script (qps) to export the image annotations as a ROIset.zip in a '/ROI Sets' folder. The ROIset.zip saving/naming convention respect the ImageJ's BIOPLib.ijm (from PTBIOP update site).

qps-export_annotations_as_ijROIs.groovy

// = CODE DESCRIPTION =
// Image annotations are saved as a ROIset.zip in a '/ROI Sets' folder, so they can be re-open in Image-j
// The ROIset.zip saving/naming convention respect the ImageJ's BIOPLib.ijm (from PTBIOP update site).
//
// == INPUTS ==
// A QuPath project, with annotations.
// 
// == OUTPUTS ==
// The annotations are saved as a ROIset.zip in a '/ROI Sets' folder, 
// 
// = DEPENDENCIES =
// QuPath 0.1.4 ,
// biop-tools-1.1.6-SNAPSHOT.jar
// 
// = INSTALLATION = 
// Open the Script in QuPath, Run (work with Run for Project)
// 
// = AUTHOR INFORMATION =
// Code written by Romain Guiet, EPFL - SV -PTECH - BIOP 
// 20191219
// 
// = COPYRIGHT =
// © All rights reserved. ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE, Switzerland, BioImaging And Optics Platform (BIOP), 2018
// 
// Licensed under the BSD-3-Clause License:
// Redistribution and use in source and binary forms, with or without modification, are permitted provided 
// that the following conditions are met:
// 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
// 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer 
//    in the documentation and/or other materials provided with the distribution.
// 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products 
//     derived from this software without specific prior written permission.
// 
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, 
// BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. 
// IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, 
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 
// LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, 
// STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF 
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
//
// TO DO : improvement would be to : don't get the ImagePlus nor open it to get the ROIs

import ij.* 
import ch.epfl.biop.qupath.utils.*
import ij.plugin.frame.RoiManager
import qupath.lib.images.servers.*

def downsampleFactor = 1

// reset Env, close images & reset roiManager
IJ.run("Close All", "");
def rm =  RoiManager.getInstance()
if(rm == null) rm = new RoiManager()
else rm.reset()

// get infos regrading the image
def images_dir = getCurrentImageData().getServer().getFile().getParent()
def image_name = getCurrentImageData().getServer().getShortServerName()
// make the output folder and file
def rois_dir =  buildFilePath(images_dir , 'ROI Sets')
mkdirs( rois_dir )
def roiset_name = image_name+'.zip'
def roiset_path = new File (rois_dir, roiset_name)

// get the image
def fullImage_annotation = PathUtils.getFullImageAnnotation()
imp = GUIUtils.getImagePlus( fullImage_annotation ,  downsampleFactor , true, true )
imp.show()
// send overlay to roiManager & save the roiset
IJ.run("To ROI Manager", "");
rm.runCommand("Save", roiset_path.toString() )