Svidro

Image exporting in QuPath
Note, this is likely a mess, and I won't be able to provide much support since I don't do this much, 
but requests are common and I have trouble tracking things down each time.

Added a script from the forum for importing binary masks as annotations.

Svidro

Scripts that are complex enough not to fit in any of the other simple categories.
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Affine transform objects between images.groovy - used with the Align images experimental tool in v0.2.0m1

Background staining check - Takes annotations, expands an area around them, checks the staining level in that area, 
then deletes all expanded areas and any original areas that violate some condition. Can help check for staining artifacts.

Classifier with GUI.groovy - User interface based macro to simplify classifying many possible channels. Also generates all
possible combinations of base classes (double, triple, etc positives).

chrislewisdev

{"version":1,"keyboard":{"keys":[{"id":0,"legend":"~\n`","state":{"x":0,"y":0,"r":0,"rx":0,"ry":0,"w":1,"h":1,"x2":0,"y2":0,"w2":0,"h2":0},"row":0,"col":0,"keycodes":[{"id":"KC_GESC","fields":[]},{"id":"KC_GRV","fields":[]},{"id":"KC_GRV","fields":[]},{"id":"KC_TRNS","fields":[]},{"id":"KC_TRNS","fields":[]},{"id":"KC_TRNS","fields":[]},{"id":"KC_TRNS","fields":[]},{"id":"KC_TRNS","fields":[]},{"id":"KC_TRNS","fields":[]},{"id":"KC_TRNS","fields":[]},{"id":"KC_TRNS","fields":[]},{"id":"KC_TRNS","fields":[]},{"id":"KC_TRNS","fields":[]},{"id":"KC_TRNS","fields":[]},{"id":"KC_TRNS","fields":[]},{"id":"KC_TRNS","fields":[]}]},{"id":1,"legend":"!\n1","state":{"x":1,"y":0,"r":0,"rx":0,"ry":0,"w":1,"h":1,"x2":0,"y2":0,"w2":0,"h2":0},"row":0,"col":1,"keycodes":[{"id":"KC_1","fields":[]},{"id":"KC_F1","fields":[]},{"id":"KC_F1","fields":[]},{"id":"KC_TRNS","fields":[]},{"id":"KC_TRNS","fields":[]},{"id":"KC_TRNS","fields":[]},{"id":"KC_TRNS","fields":[]},{"id":"KC_TRNS","fields":[]},{"id":"KC_TRNS","fields":[]},{"id"

Svidro

Collections of scripts to alter object colors harvested mainly from Pete, but also picked up from the forums
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Change IF channel color.groovy - Change the LUT for individual channels. Does not work with OpenSlide servers (check Image tab).

Change colors by subclass.groovy - Detection object color adjustment when using subclasses.

Change subcellular detection color - Hugely useful when working with subcellular detections as, by default, they are a derived class
and cannot be altered directly through the Annotation tab interface.

Svidro

Collections of scripts harvested mainly from Pete, but also picked up from the forums

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Accessing dynamic measurements.groovy - Most annotation measurements are dynamically created when you click on the annotation, and 
are not accessible through the standard getMeasurement function. This is a way around that.

Affine transformation.groovy - access more accurate measurements for the affine transformation used in the image alignment (m5/m6+)

Alignment of local cells.groovy - check neighborhood for similarly aligned cells