petebankhead

/**
 * Script to open the QuPath extensions directory.
 * This is handy if you want to add/remove extensions manually.
 * 
 * Since it depends on java.awt.Desktop, it may not be supported on all platforms.
 * 
 * @author Pete Bankhead
 */

petebankhead

/**
 * Script to update cell measurement names for a multichannel fluorescence image
 * to incorporate actual stored channel names, rather than the defaults of
 * 'Channel 1', 'Channel 2' etc.
 *
 * @author Pete Bankhead
 */

import qupath.lib.scripting.QPEx

petebankhead

/**
 * Demo script showing a simple method of assigning classifications for a multichannel fluorescence image.
 *
 * Note that at the time of writing, this requires the most recent (pre-release) QuPath version.
 * See https://petebankhead.github.io for more information.
 *
 * The channel names here refer to the sample image 'LuCa-7color_[13860,52919]_1x1component_data.tif'
 * from Perkin Elmer, after running 'Update measurement names.groovy' script.
 *
 * The original image is part of Bio-Formats demo data, under Creative Commons Attribution 4.0 International License

petebankhead

/**
 * Helper script for QuPath to find objects with one or more classifications.
 *
 * @author Pete Bankhead
 */

// Insert as many or few classifications here as required
selectObjects {checkForClassifications(it.getPathClass(), 'CD8', 'FoxP3')}
print 'Selected ' + getSelectedObjects().size()

petebankhead

/**
 * Flip the ROIs for QuPath objects (usually annotations) vertically or horizontally.
 *
 * This creates new objects that are then added to the current image hierarchy.
 *
 * This also shows the method by which any arbitrary AffineTransform may be
 * applied to an object by scripting.
 * 
 * Note: This version is updated for QuPath v0.2.
 *

petebankhead

/**
 * Script to help with annotating tumor regions, separating the tumor margin from the center.
 *
 * Here, each of the margin regions is approximately 500 microns in width.
 *
 * NOTE: This version has been updated for v0.2.0-m6 and to use Java Topology Suite.
 *
 * @author Pete Bankhead
 */

petebankhead

/**
 * Export an image thumbnail & overlay as separate images.
 *
 * The overlay is written as PNG with transparent background.
 *
 * @author Pete Bankhead
 */

import qupath.lib.regions.RegionRequest

petebankhead

/**
 * Set a MeasurementMapper in QuPath v0.2 to control the display in a script.
 *
 * Revised version of a script for v0.1.2.
 * 
 * @author Pete Bankhead
 */

import qupath.lib.gui.tools.MeasurementMapper

petebankhead

getTMACoreList().each {
    it.clearMetadata()
}
fireHierarchyUpdate()

petebankhead

// Remove really tiny objects (here, with areas <= 1 pixel.... and also lines)
// They can be created when using the wand/brush & subtracting almost all of a region (for example)
tinyAreas = getAnnotationObjects().findAll {
    return !it.isPoint() && it.getROI().getArea() <= 1
}
print 'Number of objects to remove: ' + tinyAreas.size()
removeObjects(tinyAreas, true)