This repository contains a QuPath extension designed to simplify the deployment of Neuro-R within QuPath, enhancing image analysis workflows for pathology research.
To install this extension, simply drag and drop the latest release into an open QuPath window, or place it in your QuPath extensions folder.
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Configure environment paths under Extensions > NeuroR Extension > Environments.
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Set your preferences for segmentation, object detection, and classification in Extensions > NeuroR Extension > Segmentation/Object Detection/Classification.
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Click the 'Generate' button next to Script Name to create a script, then edit the generated script name as needed.
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Press the 'Create Script!' button to open the Script Editor with your custom script.
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Start inference by pressing the 'Run' button at the bottom right of the Script Editor.
- Clone this repository and open it in IntelliJ IDEA.
- Clone QuPath's repository, then use "Link Gradle Project" to import the QuPath directory.
- Add the line
includeFlat 'qupath-extension-neuror'toqupath/settings.gradle. - Ensure that the value of
gradle.ext.qupathVersioninqupath/settings.gradleis equal to the value specified by inqupath-extension-neuror/settings.gradle. - Create a Run Configuration to launch QuPath.
With these steps, you should be able to see this extension automatically loaded into QuPath when running it in IntelliJ IDEA.
- Open the terminal in IDEA, then
cdto the extension directory. - Run
./gradlew build
Created JARs will be in qupath-extension-neuror/build/libs/.
If you encounter java.lang.ClassNotFoundException: org.slf4j.LoggerFactory error while trying to run QuPath, try restarting IDEA.
This work was supported by a grant from the Korea Health Technology R&D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health & Welfare, Republic of Korea (grant number: HI21C1137).