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

petebankhead

/**
 * Convert detected nuclei to cells and add measurements.
 * Written for v0.3.x to answer 
 * https://forum.image.sc/t/is-it-possible-to-modify-the-cell-expansion-parameter-after-cells-have-been-detected/61665
 * 
 * Because adding intensity measurements is especially awkward, this should be improved in a future version.
 *
 * Note that the cell measurements are *not* equivalent to QuPath's built-in cell detection.
 * They are calculated in a different way and have different names.
 * 

petebankhead

/**
 * QuPath script to threshold a single channel of an image.
 * This can also be useful to convert a binary image into QuPath annotations.
 *
 * First written for https://forum.image.sc/t/rendering-wsi-as-overlay-on-top-of-another-wsi/52629/24?u=petebankhead
 *
 * @author Pete Bankhead
 */

int channel = 0                              // 0-based index for the channel to threshold

petebankhead

/**
 * Helper script to extract manually-annotated photos from an image,
 * e.g. to help with digitising a photo album based upon scanning each page.
 *
 * The main thing this will do is to use the annotated polygons and perform
 * a perspective transform to unwarp the photos.
 *
 * It can be applied in batch to many images.
 *
 * To use it

petebankhead

/**
 * QuPath script to group together clusters identified with Delaunay clustering.
 * This provides several options:
 * - clusters as classifications
 * - clusters as object names
 * - clusters as measurement values
 * You should comment out the lines you don't want.
 *
 * Note that this is *very* rough and not guaranteed to work.
 * It was written for https://forum.image.sc/t/cell-classification-within-a-segmented-region-in-histology-images/55507/21?u=petebankhead

petebankhead

/**
 * Script to help track down memory leaks.
 * Uses JavaCPP, some useful info at https://javadoc.io/static/org.bytedeco/javacpp/1.5.5/org/bytedeco/javacpp/Pointer.html
 *
 * @author Pete Bankhead
 */

import org.bytedeco.javacpp.Pointer

System.gc()

petebankhead

/**
 * Find the 'brightest' circle in a fluorescence image in QuPath v0.2.
 *
 * This could be used for creating ROIs in a TMA image where each core is a separate image.
 *
 * @author Pete Bankhead
 */


import ij.plugin.filter.RankFilters

petebankhead

/**
 * Slightly involved script to threshold a fluorescence multi-channel image
 * in QuPath v0.2 to generate a new region of interest annotation.
 *
 * Might be used whenever there is too much variation for a threshold classifier
 * to work.
 *
 * @author Pete Bankhead
 */

petebankhead

/**
 * Assign an ID to cells in QuPath using several different methods.
 * This is useful if you want to export cell data from QuPath, process it elsewhere, 
 * and then bring the results back into QuPath again.
 * 
 * Note: After checking the advantages/disadvantages, you should only need to use 
 * one of these. If it fits with your uses, my preference would be 3 or 4.
 */

// Get the cell objects (all options start here)