petebankhead

/**
 * A basic GUI to help monitor memory usage in QuPath.
 *
 * This helps both to find & address out-of-memory troubles by
 *   1. Showing how much memory is in use over time
 *   2. Giving a button to clear the tile cache - which can be
 *      using up precious memory
 *   3. Giving quick access to control the number of threads used
 *      for parallel processing
 *

petebankhead

/**
 * QuPath script to calculate areas (e.g. of tumor) based upon classified cells only.
 *
 * It works by using a distance transform applied to binary images generated from the
 * objects of each class, and then assigns each pixel to the closest object.
 *
 * Having done this, new annotations are generated for these regions.
 *
 * WARNINGS!
 * - This will remove *all* previous annotations & replace them with new annotations

petebankhead

/**
 * Script to combine results tables exported by QuPath.
 *
 * This is particularly intended to deal with the fact that results tables of annotations can produce results
 * with different column names, numbers and orders - making them awkward to combine later manually.
 *
 * It prompts for a directory containing exported text files, and then writes a new file in the same directory.
 * The name of the new file can be modified - see the first lines below.
 *
 * Note: This hasn't been tested very extensively - please check the results carefully, and report any problems so they

petebankhead

/*
 * QuPath v0.1.2 has some bugs that make exporting annotations a bit annoying, specifically it doesn't include the 'dot' 
 * needed in the filename if you run it in batch, and it might put the 'slashes' the wrong way on Windows.
 * Manually fixing these afterwards is not very fun.
 * 
 * Anyhow, until this is fixed you could try the following script with Run -> Run for Project.
 * It should create a new subdirectory in the project, and write text files containing results there.
 *
 * @author Pete Bankhead
 */

petebankhead

/**
 * Script to set cell intensity sub-classifications based on an arbitrary number
 * of thresholds.
 *
 * Note: Because QuPath's dynamic measurements only care about negative/positive or
 *       negative/1+/2+/3+, any further classifications (e.g. 4+, 5+) won't be part of the
 *       summary scores (e.g. H-score or even Positive %)!
 *       Be warned and be careful!
 *
 * For 3 thresholds or fewer, the built-in setCellIntensityClassifications method is preferable.

petebankhead

/**
 * A script to simplify the ROIs of all selected annotation objects.
 *
 * @author Pete Bankhead
 */

import qupath.lib.gui.QuPathGUI
import qupath.lib.objects.PathAnnotationObject
import qupath.lib.roi.PolygonROI
import qupath.lib.roi.ShapeSimplifierAwt

petebankhead

/**
 * Request an image from QuPath as an (ImageJ) ImagePlus.
 * The aim is to avoid the (arbitrary) size threshold in v0.1.2 of QuPath.
 *
 * @author Pete Bankhead
 */

import ij.IJ
import qupath.imagej.gui.IJExtension
import qupath.imagej.helpers.IJTools

petebankhead

/**
 * Demonstration of how to use ImageJ + QuPath to detect stained regions in
 * a brightfield image.
 *
 * @author Pete Bankhead
 */


import ij.CompositeImage
import ij.IJ

petebankhead

/**
 * Create a region annotation with a fixed size in QuPath, based on the current viewer location.
 *
 * @author Pete Bankhead
 */

import qupath.lib.objects.PathAnnotationObject
import qupath.lib.objects.classes.PathClassFactory
import qupath.lib.roi.RectangleROI
import qupath.lib.scripting.QPEx

petebankhead

/**
 * Script to export binary masks corresponding to all annotations of an image,
 * optionally along with extracted image regions.
 *
 * Note: Pay attention to the 'downsample' value to control the export resolution!
 *
 * @author Pete Bankhead
 */

import qupath.lib.images.servers.ImageServer