QuPath script to export images corresponding to all the annotation bounding boxes in an image

QuPath-Export images for annotation bounding boxes.groovy

/**
 * QuPath script to export images corresponding to all the annotation bounding boxes in an image.
 * Written for QuPath v0.4.3.
 */

// Export at full resolution (or change this value)
double downsample = 1.0

// Export to a subdirectory of the current project
def dir = buildPathInProject("export")
mkdirs(dir)

// Loop through annotations and export
def server = getCurrentServer()
def annotations = getAnnotationObjects()
for (def annotation in annotations) {
    def request = RegionRequest.createInstance(
        server.getPath(),
        downsample,
        annotation.getROI()
    )
    def name = getCurrentImageNameWithoutExtension()
    def outputName = "${name}-${request.x} [${request.y},${request.width},${request.height}].tif"
    def path = buildFilePath(dir, outputName)
    println path
    writeImageRegion(server, request, path)
}