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QuPath Py4J extension 🐍

This extension aims to provide a link between QuPath and Python using Py4J

Installation

If you're using QuPath v0.6.0-rc3 (release candidate 3), then you don't need to install this — it's included by default.

You can install this extension the same as other QuPath extensions, as described in the docs.

Usually this involves using the built-in extension manager, or by downloading a build of the extension from the releases and dragging this onto a QuPath window.

Usage

To start a Py4J gateway from QuPath, you can either click the Python icon on the QuPath toolbar, or use the menu item Extension -> Py4J -> Start Py4J Gateway.

This dialog allows you to specify the port used for the websocket connection, and an optional authentication token:

A dialog box for the QuPath Py4J extension. A brief description of the purpose of a gateway, followed by "Port" and "Token" text fields followed by "Random" and "Copy" buttons, with "Cancel" and "OK" buttons at the bottom of the dialog.

Once a gateway is started, you can connect from a Python process using qubalab:

from qubalab.qupath import qupath_gateway
gateway = qupath_gateway.create_gateway(port=25333)

gateway.getExtensionVersion() # query the verison of the QuPath Py4J extension

Further documentation can be found in the qubalab project.

Development

It's recommended to use the extension setup described in the QuPath extension template for this extension.