QuPath stitching extension

Welcome to the stitching extension for QuPath!

This extension supports stitching individual fields of view into a larger image. This includes Vectra images where the position information is encoded in the file name or TIFF tags.

Installing

To install the stitching extension, you can:

• Open the QuPath extension manager and install the extension from there (recommended).
• Or download the latest qupath-extension-stitching-[version].jar file from releases and drag it onto the main QuPath window.

If you haven't installed any extensions before, you'll be prompted to select a QuPath user directory. The extension will then be copied to a location inside that directory.

You might then need to restart QuPath (but not your computer).

You can then stitch images in QuPath by clicking on Extensions -> Stitch images. The default parameters should be sufficient to stitch Vectra images.

Additionally, you can use the extension in a script (see the sample-scripts folder of this repository).

Building

You can build the extension using OpenJDK 21 or later with

./gradlew clean build

The output will be under build/libs. You can drag the jar file on top of QuPath to install the extension.

Running tests

You can run the tests with

./gradlew test

Running benchmarks

You can run the benchmarks with

./gradlew jmh