https://github.com/qupath/qupath-extension-wsinfer

QuPath extension to work with WSInfer - https://wsinfer.readthedocs.io/
https://github.com/qupath/qupath-extension-wsinfer

Last synced: 15 days ago
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QuPath extension to work with WSInfer - https://wsinfer.readthedocs.io/

• Host: GitHub
• URL: https://github.com/qupath/qupath-extension-wsinfer
• Owner: qupath
• License: apache-2.0
• Created: 2023-07-10T11:17:32.000Z (almost 2 years ago)
• Default Branch: main
• Last Pushed: 2023-12-04T11:27:22.000Z (over 1 year ago)
• Last Synced: 2023-12-04T12:28:58.166Z (over 1 year ago)
• Language: Java
• Size: 509 KB
• Stars: 14
• Watchers: 0
• Forks: 5
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG.md
  • License: LICENSE

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README

        
[![Preprint](https://zenodo.org/badge/DOI/10.48550/arXiv.2309.04631.svg)](https://doi.org/10.48550/arXiv.2309.04631)

[![Extension docs](https://img.shields.io/badge/docs-qupath_wsinfer-red)](https://qupath.readthedocs.io/en/stable/docs/deep/wsinfer.html)

[![Forum](https://img.shields.io/badge/forum-image.sc-green)](https://forum.image.sc/tag/wsinfer)

[![Downloads (latest release)](https://img.shields.io/github/downloads-pre/qupath/qupath-extension-wsinfer/latest/total)](https://github.com/qupath/qupath-extension-wsinfer/releases/latest)

[![Downloads (all releases)](https://img.shields.io/github/downloads/qupath/qupath-extension-wsinfer/total)](https://github.com/qupath/qupath-extension-wsinfer/releases)

# QuPath WSInfer extension

This repo contains the QuPath extension that adds support for the [WSInfer Model Zoo](https://wsinfer.readthedocs.io).

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](https://arxiv.org/abs/2309.04631)

**If you use this extension, please cite both the [WSInfer preprint](https://arxiv.org/abs/2309.04631) and the [QuPath paper](https://qupath.readthedocs.io/en/0.4/docs/intro/citing.html)!**

## Installation

Download the latest version of the extension from the [releases page](https://github.com/qupath/qupath-extension-wsinfer/releases).

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

See [the QuPath docs](https://qupath.readthedocs.io/en/0.5/docs/intro/extensions.html) 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](https://qupath.readthedocs.io/en/stable/docs/deep/wsinfer.html).

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)](https://forum.image.sc/tag/wsinfer) - and tag both `wsinfer` and `qupath` so we notice.