Merge pull request #38 from qupath/petebankhead-patch-1

Update README.md

Author: petebankhead

README.md

@@ -1,12 +1,23 @@
-# QuPath extension WSInfer
+[![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)
 
-This repo contains the extension to work with WSInfer models in QuPath.
 
-This helps make deep learning-based patch classification in pathology images easy and interactive.
+# QuPath WSInfer extension
 
-See https://wsinfer.readthedocs.io for details.
+This repo contains the QuPath extension that adds support for the [WSInfer Model Zoo](https://wsinfer.readthedocs.io).
 
-> **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)!**
+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 <br/>
+> *Open and reusable deep learning for pathology with WSInfer and QuPath*.  <br/>
+> 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
 
@@ -19,20 +30,6 @@ Then drag & drop the downloaded .jar file onto the main QuPath window to install
 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).
 
-Briefly: after selecting a WSInfer model, you'll need to select one or more tiles to use for inference.
-The easiest way to do this is generally to draw an annotation, and leave it up to QuPath to create the tiles.
-
-Pressing run will download the model and PyTorch (if necessary), then run the model across the tiles.
-
-You can see the results in the form of measurement maps, as a results table, or as colored tiles in the QuPath viewer.
-
-> Tip: To see the tiles properly, you'll need to ensure that they are both displayed and filled in the viewer (i.e. ensure the two buttons showing three green objects are selected).
-
-## Additional options
-
-It's worth checking out the *Additional options* to see where models will be stored.
-
-You can also use this to select whether inference should use the CPU or GPU - if a GPU is available and compatible.
-
-> GPU acceleration is selected by choosing *MPS* on an Apple Silicon Mac, for *Metal Performance Shaders*.
+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.