qupath

QuPath MONAILabel extension

Download QuPath from: https://qupath.github.io/ and then install monailabel plugin using one of the following methods.

From Binaries

Download qupath-extension-monailabel-0.3.1.jar and drag the jar on top of the running QuPath application window (black screen area) to install the extension. If you are have previously installed then make sure to remove/uninstall the extension before updating.

Development in progress. If you are using latest MONAI Label, please build from source or use latest QuPath plugin available from here and vice versa.

Building from source

You can build the latest extension jar using OpenJDK 11 or later with gradle

gradle clean build

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

Using Plugin

• Make sure MONAILabel Server URL is correctly through Preferences.
• Open Sample Whole Slide Image in QuPath (which is shared as studies for MONAILabel server)
• Add/Select Rectangle ROI to run annotations using MONAI Label models.
• For Interative model (e.g. DeepEdit) you can choose to provide Positive and Negative points through Annotation panel.