petebankhead

/**
 * Split a rectangle into equal parts along its longest dimension.
 * Rotated rectangles are supported.
 * 
 * Written for https://forum.image.sc/t/how-to-divide-annotation-roi-into-equal-dimension-bins/51563/8
 *
 * @author Pete Bankhead
 */

// Number of regions to create

petebankhead

/**
 * This script generates a point annotation containing randomly generated points in QuPath v0.2 or v0.3.
 * 
 * These can optionally be constrained to fall within the selected ROI, within the entire image, 
 * or within the largest circle that falls within the entire image.
 * 
 * For the original motivation behind this script, see https://forum.image.sc/t/digital-chalkley-point-graticule-overlay/51211
 * 
 * @author Pete Bankhead
 */

petebankhead

/**
 * Remove detections that have ROIs that touch the border of any annotation ROI in QuPath v0.2.
 *
 * Note that there are some non-obvious subtleties involved depending upon how ROIs are accessed -
 * see the 'useHierarchyRule' option for more info.
 *
 * Written for https://forum.image.sc/t/remove-detected-objects-touching-annotations-border/49053
 *
 * @author Pete Bankhead
 */

petebankhead

/**
 * Copy QuPath annotations across z-slices or timepoints.
 *
 * This is a convenience script to help (slightly) annotating in 3D or 4D images.
 *
 * (This hasn't been very thoroughly checked - if it doesn't seem to work for you, 
 * it might just not work... you can use the comments to discuss this)
 *
 * @author Pete Bankhead
 */

petebankhead

/**
 * QuPath script to visualize annotations on all z-slices, not just the current one.
 *
 * This is handy when annotating structures visible across z-slices, but where they might
 * appear with better contrast in different slices.
 * 
 * @author Pete Bankhead
 */

petebankhead

/**
 * Run cell detection using the DeepCell Kiosk ImageJ plugin from
 * https://github.com/vanvalenlab/kiosk-imagej-plugin
 *
 * For authorship & license of Deep Cell see http://deepcell.org
 *
 * To use the script, drag the Kiosk plugin on top of QuPath to make it available as an extension.
 * Then select a (small!) region of interest in a compatible image and run this script from QuPath's script editor.
 *
 * Note that the image needs to be in a compatible format -

petebankhead

server = getCurrentServer()
xml = server.dumpMetadata()
print groovy.xml.XmlUtil.serialize(xml)

petebankhead

/**
 * General template for using ImageJ to detect ROIs from QuPath.
 *
 * Note the results of this script are terrible; it just applies a threshold per tile (calculated per tile).
 * Its purpose is to show the process... not to do something useful in itself.
 *
 * However, in principle you just need to change the 'detectRois' method to something better to have something
 * that might be worthwhile.
 *
 * @author Pete Bankhead

petebankhead

/**
 * Update the image name in the ImageServer metadata to match with the image name in the project.
 * 
 * This can be used (with caution!) to work around the fact that v0.2.x uses the name from the server 
 * in measurement tables when they are export - not the project.
 * 
 * Using 'Run -> Run for project' to apply it to all images in a project.
 * Best back up (as always) before doing anything that will change data files, but an additional 
 * safeguard here is that the original metadata can still be accessed via server.getOriginalMetadata(), 
 * and can be reset by double-clicking the 'Metadata changed' entry under the 'Image' tab.

petebankhead

/** 
 * Import images from .qpdata files into a new project in QuPath v0.2.x.
 * 
 * The purpose of this is to help recover data from files that were saved outside a project.
 * It may not work for all images, but should work for most 'straightforward' examples (i.e. a single image per image file).
 * 
 * If your .qpdata files are already part of a v0.1.2 project, use 'File -> Project... -> Import images from v0.1.2' instead.
 * If your .qpdata files are already part of a v0.2.0 project, use 'File -> Project... -> Add images' and add the .qpproj file instead.
 * 
 * Warning! This hasn't been very extensively tested (I always use projects from the start...).