petebankhead

/**
 * Sum the area of detections with a specified classification.
 * Written for QuPath v0.3.2.
 *
 * @author Pete Bankhead
 */

// Define name of the class of detection objects
def className = 'Positive'

petebankhead

/**
 * Rotate all objects in an image by 180 degrees, translating them so they 
 * remain within the image.
 * 
 * Written for QuPath v0.3.2
 * 
 * See https://forum.image.sc/t/overlaying-h-e-and-tissue-annotations-in-qupath/71861/3
 * 
 * @author Pete Bankhead
 */

petebankhead

/**
 * Export images of individual cell nuclei, with corresponding binary masks.
 * Written for QuPath v0.3.2.
 * 
 * See https://forum.image.sc/t/generate-bounding-box-images-and-their-corresponding-xml-json-files-with-each-separate-annotation/68119/
 *
 * @author Pete Bankhead
 */

import qupath.lib.images.servers.LabeledImageServer

petebankhead

/**
 * Simple script for QuPath v0.3.2 that loops through all available channels, 
 * displaying them in turn for 1 second.
 *
 * Written for https://forum.image.sc/t/how-do-i-script-qupath-to-change-the-displayed-channel/67216
 *
 * @author Pete Bankhead
 */

def viewer = getCurrentViewer()

petebankhead

/**
 * Export QuPath annotations in GeoJSON using calibrated pixel sizes 
 * (rather than pixel units).
 *
 * Written for QuPath v0.3.2
 * 
 * @author Pete Bankhead
 */

// Define export directory (or null if we don't want to export, but just print the GeoJSON)

petebankhead

/**
 * Script to add density map values to *some* detection centroids in QuPath v0.3,
 * limited to only use a subset of the detections on the image.
 *
 * It does this by copying the relevant objects and adding them to a temporary ImageData.
 * 
 * Note that this hasn't been tested very much... and assumes a 2D image.
 * At the very least, you should use 'Measure -> Show measurement maps' as a sanity check.
 *
 * Written for https://forum.image.sc/t/qupath-number-of-detections-per-tile/64603/14

petebankhead

/**
 * Script to add density map values to detection centroids in QuPath v0.3.
 * 
 * Note that this hasn't been tested very much... and assumes a 2D image.
 * At the very least, you should use 'Measure -> Show measurement maps' as a sanity check.
 *
 * Written for https://forum.image.sc/t/qupath-number-of-detections-per-tile/64603/10
 *
 * @author Pete Bankhead
 */

petebankhead

/*
 * Export annotations representing instance labels from an image.
 * 
 * This supports exporting regions of an image (rather than the whole thing) 
 * defined using the annotation shape (i.e. rectangle) or classification.
 * 
 * See the comments for more information, and parameters to adjust.
 *
 * Note that the instance labels are applied globalled, so if multiple distinct 
 * regions are export, the labels are not guaranteed to start from 1 or be consecutive 

petebankhead

def server = getCurrentServer()
def manager = server.getManager()
def annotations = []
for (def region in manager.getRegions()) {
    def roi = ROIs.createRectangleROI(region)
    def server2 = manager.getServer(region, 1)
    def name = server2.getMetadata().getName()
    def pathObject = PathObjects.createAnnotationObject(roi)
    pathObject.setName(name)
    annotations << pathObject

petebankhead

/**
 * Script to set the name of a cell to include the classifications of 
 * all annotations that contain it, sorted by area.
 * The purpose of this is to include information about all the annotations 
 * containing the cell in a measurement table, rather than only the immediate parent.
 * 
 * Written for QuPath v0.3.
 */

// Get the current hierarchy and all cells