QuPath Cloud Healthcare API Extension

The QuPath Cloud Healthcare API provides viewing whole-slide images online without full downloading and synchronize annotations with the help of Google Cloud Healthcare API.

Installation:

1. Install QuPath v0.3.0 from here.
2. Download the latest JAR from the releases tab.
3. When you install QuPath, folder for extensions is set to /home/user/QuPath/extensions by default (in Linux). You can put the JAR in this folder or just drag-and-drop it in the QuPath window.

If you already have QuPath and want to install the new version a new QuPath user directory is recommended. You can set another user directory by going to Edit -> Preferences -> Set another user directory in QuPath. Also, you can delete the previous extension version, if you don't want to use another QuPath user directory.

Setting up project to use DICOM cloud:

1. Create empty project in QuPath.
2. Click Cloud on the button bar. Login with OAuth in your default browser with your account which has access permission to Cloud Healthcare API (1 time).
3. Select the desired Project and click NEXT in extension window.
4. Select an existing Dataset or create a new one. Steps to create a new Dataset:
   1. Click New Dataset.
   2. Input the Dataset name.
   3. Select the location where the Dataset should be stored.
   4. Click CREATE.
   5. Click NEXT.
5. Select an existing DICOM Store which contains whole-slide images or create a new one. Steps to create a new DICOM Store:
   1. Click New DICOM Store.
   2. Input the DICOM Store name.
   3. Click CREATE.
   4. Click OK.
6. Upload dicomized images into created DICOM Store and Dataset in chosen Location:
   1. If you want to use the embedded wsi-to-dicom-converter in the qupath-chcapi-extension, just add images to the project. When you click Synchronize images will be dicomized and uploaded.
   2. Alternatively you can use OrthancWSIDicomizer. Once source images have been dicomized, you can upload them via gcloud.
7. Click Synchronize on the button bar in QuPath to synchronize DICOM Store with your project.

Extension saved in your chosen dicom store for existing project and saved your access permission on the computer.
Supported formats for qupath-chcapi-extension and pathology test data you can see here.

Synchronization annotations:

1. Add/Edit image annotations in existing project.
2. Save changed annotations via File->Save.
3. Click Synchronize (annotations will be uploaded in chosen DICOM Store).
4. If DICOM Store contains dicomized annotations that are locally absent they will be downloaded.
5. If DICOM Store contains different versions of annotations for the same images, user will be presented window with conflict list and asked to resolve them (with defaults set based on last modified timestamp).
6. (Re)open annotated image - need to reload ImageData containing annotations.

Note:

QuPath uses embedded Java and may cause some errors. If you get any errors with it, follow these steps:

1. Download and install Java SE Development Kit 11.
2. Open QuPath/app folder in the terminal.
3. Launch QuPath with following parameters java -Djava.library.path=. -jar qupath-0.2.0-m10.jar

Compilation:

Perform the following steps for compiling extension and packaging to qupath-chcapi-extension.jar:

1. git clone https://github.com/qupath/qupath.git in the terminal in your local folder (for adding dependencies from QuPath).
2. git checkout v0.2.0-m10 to switch to QuPath v0.2.0-m10.
3. Add apply plugin: 'maven' string in build.gradle(Build all projects - all projects point) in qupath folder.
4. ./gradlew install in qupath folder in the terminal.
5. Copy openslide folder to .m/repository/org/ from qupath/maven/repo/org/ folder. It's necessary to copy openslide dependencies to the local maven repository.
6. git clone https://github.com/GoogleCloudPlatform/qupath-chcapi-extension.git
7. mvn package in qupath-chcapi-extension folder in the terminal (for packaging to jar).

Resulting qupath-chcapi-extension-X.Y.Z.jar will be put into qupath-chcapi-extension/target folder.

License:

This extension is licensed under GPL v3. Full license text is available in LICENSE.