QuPath WSInfer extension

This repo contains the QuPath extension that adds support for the WSInfer Model Zoo.

Together, QuPath & WSInfer aim to make deep learning-based patch classification easy and interactive for pathology images.

To find out more, check out our preprint on arXiv:

Jakub R. Kaczmarzyk, Alan O'Callaghan, Fiona Inglis, Tahsin Kurc, Rajarsi Gupta, Erich Bremer, Peter Bankhead, Joel H. Saltz
Open and reusable deep learning for pathology with WSInfer and QuPath.
arXiv, 2023

If you use this extension, please cite both the WSInfer preprint and the QuPath paper!

Installation

Download the latest version of the extension from the releases page.

Then drag & drop the downloaded .jar file onto the main QuPath window to install it.

See the QuPath docs for more info about installing & updating extensions.

Usage

The WSInfer extension adds a new menu item to QuPath's Extensions menu, which can be used to open a WSInfer dialog.

The dialog tries to guide you through the main steps, from top to bottom. For a step-by-step guide,see ReadTheDocs.

And if things don't go to plan or you want to discuss more, please post your questions on the Scientific Community Image Forum (image.sc) - and tag both wsinfer and qupath so we notice.