petebankhead

/**
 * Groovy script to generate a batch script to launch QuPath while setting the PATH 
 * from a conda environment.
 * 
 * This is useful to add GPU support with Deep Java Library (DJL) without needing to install 
 * CUDA system-wide.
 * 
 * This script was written for QuPath v0.5.
 * You should read the top part and change the variables to match what you need.
 */

petebankhead

/**
 * QuPath v0.4.3 script to threshold probability outputs from a pixel classifier.
 *
 * By default, converting the pixel classifier output to probabilities will always
 * apply a softmax operation and take the class with the highest probability.
 *
 * This script provides an alternative, whereby you can specify a probability threshold
 * for one or more channels, and threshold to create objects from that.
 * Using a higher threshold can then restrict the object creation of more confident predictions.
 *

petebankhead

/**
 * 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")

petebankhead

/**
 * Create a convex or concave hull annotation from the selected objects.
 *
 * The calculations are performed using Java Topology Suite's 'ConcaveHullOfPolygons' class -
 * see https://locationtech.github.io/jts/javadoc/org/locationtech/jts/algorithm/hull/ConcaveHullOfPolygons.html
 *
 * This was written for QuPath v0.4.3.
 * If it's useful enough, a similar feature might be added to QuPath directly in the future.
 *
 * @author Pete Bankhead

petebankhead

/**
 * Create a point annotation showing equally-spaced splits
 * along a polyline or simple polygon (i.e. no holes or
 * self-intersections).
 *
 * See https://forum.image.sc/t/divide-free-hand-lines-at-regular-interval/79845/4
 *
 * Written for QuPath v0.4.3 using JTS.
 *
 * @author Pete Bankhead

petebankhead

/**
 * Create fixed-sized square annotations around the points of a selected 
 * point annotation.
 * 
 * Written for QuPath v0.4 and v0.5.
 * See https://forum.image.sc/t/is-it-possible-to-create-annotations-on-click/79270
 * 
 * Edited 12/2023 to support multiple selected point annotations (not just one).
 *
 * @author Pete Bankhead

petebankhead

/**
 * Constrain all selected annotations so that they fall inside unselected annotations.
 *
 * This is intended for a case where
 * - you have some annotations that define a region of interest (e.g. all tissue)
 * - some other annotations that partially overlap the first annotations, but which *should* be inside
 *
 * If you select the second annotations and run this script, it should remove the parts that are outside the first
 * annotations - effectively cleaning up the image.
 *

petebankhead

/**
 * Create a convex hull annotation surrounding all selected objects.
 * 
 * Note that this
 * - was written using QuPath v0.4.x (but probably works in some earlier releases)
 * - doesn't work very well for ellipse objects, but should be ok with other shapes
 * - assumes that you only have a 2D image (you'd need to change the 'image plane' part for z-stacks or timeseries)
 * 
 * It was written for https://forum.image.sc/t/qupath-script-command-to-draw-polygon-annotation-from-points/76833
 *

petebankhead

/**
 * QuPath script to extract a stack/hyperstack + overlay and send it to ImageJ.
 *
 * This will either extract a hyperstack for the bounding box of the current selected object,
 * or for the entire image if no object is selected.
 *
 * Written for https://forum.image.sc/t/qupath-how-to-send-multiple-annotations-containing-more-annotations-to-imagej-with-all-z-slices-and-re-name/76107
 *
 * Tested (to an extent...) with QuPath v0.4.2
 *

petebankhead

/**
 * Add pixel classifier measurements to all cells in an image.
 * 
 * This is intended to overcome the fact that measurements can be quite slow because they aren't parallelized.
 * 
 * Written for QuPath v0.3.2.
 * See https://forum.image.sc/t/qupath-measure-pixel-classifier-area-per-cell-detection-for-wsis/72701
 * 
 * Warning! This hasn't been extensively tested - please report any problems on the forum.
 *