petebankhead

/**
 * Example QuPath startup script to open the brightness/contrast dialog & channel viewer,
 * optionally setting their location.
 *
 * Originally posted at https://forum.image.sc/t/saving-window-layout/103763/3
 *
 * Written for QuPath v0.5.x
 */

petebankhead

/**
 * Quick Groovy script to get the location of a window in a JavaFX application.
 * Originally posted at https://forum.image.sc/t/saving-window-layout/103763/3
 * Written for QuPath v0.5.x
 */

import javafx.stage.Window

String title = "Brightness & contrast"

petebankhead

/**
 * QuPath script to help convert one or more images to PNG or JPEG,
 * while also reducing the dimensions and file size.
 *
 * The purpose is to help convert images for websites in a way that balances file size with quality.
 *
 * Given an image file or directory containing multiple files (usually screenshots), this will:
 * - Strip away any unnecessary alpha channel
 * - Resize so that the width and height are <= a specified maximum dimension
 * - Iteratively try to convert the image to PNG and/or JPEG by

petebankhead

/**
 * QuPath script to copy images into a project.
 * This is used to help make the project directory self-contained.
 *
 * By default, local files are copied into an 'images' subdirectory of the project.
 *
 * Limitation: This only handles local files that are currently outside the project directory,
 *             and excludes images that are known to have 'multipart' files (e.g. dicom, mrxs, vsi & zarr).
 *
 * Warning: This has not been very extensively tested!

petebankhead

/**
 * QuPath script to create concentric rings around an annotation.
 */

// Number of rings to create
int nRings = 5

// Define distance in µm, then convert (or just go straight to defining in pixels)
double distanceMicrons = 100
double distancePixels = distanceMicrons / getCurrentServer().getPixelCalibration().getAveragedPixelSizeMicrons()

petebankhead

/**
 * Script to convert all polyline annotations to polygons in QuPath.
 * Written for QuPath v0.5 (may work in other versions).
 */

def lineObjects = getAnnotationObjects().findAll {it.getROI().isLine()}
def polygonObjects = []
def selectedObjects = getSelectedObjects() as List
for (lineObject in lineObjects) {
    def line = lineObject.getROI()

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