QuPath MonaiLabel Server Authentication

[Mena-SA-Kamel]

Hello All,

I am trying to connect QuPath to a MonaiLabel server running on a remote host. The host requires authentication via some credentials. I downloaded the MonaiLabel extension for QuPath using the instructions provided.

However, I am getting a 401 error when I attempt to get the annotations. I suspect that is because I did not authenticate to the server. Is there a way to specify the authentication token to connect my local QuPath instance to the remote MonaiLabel server?

Thanks,
Mena

Here are the QuPath logs for your reference:
INFO: MONAI Label Annotation - URL => https://<>/mk-monai/port/8000/info/ INFO: {"error":"unauthorised access"} ERROR: MONAILabel: (GET https://<>/mk-monai/port/8000/info/) 401 ERROR: MONAILabel java.io.IOException: (GET https://<>/mk-monai/port/8000/info/) 401 at qupath.lib.extension.monailabel.RequestUtils.request(RequestUtils.java:59) at qupath.lib.extension.monailabel.MonaiLabelClient.info(MonaiLabelClient.java:131) at qupath.lib.extension.monailabel.commands.RunInference.run(RunInference.java:78) at qupath.lib.gui.ActionTools.lambda$createAction$1(ActionTools.java:724) at org.controlsfx.control.action.Action.handle(Action.java:423) at org.controlsfx.control.action.Action.handle(Action.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.control.MenuItem.fire(MenuItem.java:459) at com.sun.javafx.scene.control.ContextMenuContent$MenuItemContainer.doSelect(ContextMenuContent.java:1385) at com.sun.javafx.scene.control.ContextMenuContent$MenuItemContainer.lambda$createChildren$12(ContextMenuContent.java:1338) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3881) at javafx.scene.Scene.processMouseEvent(Scene.java:1874) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2607) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:411) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:301) at java.base/java.security.AccessController.doPrivileged(Unknown Source) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:450) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:424) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:449) at com.sun.glass.ui.View.handleMouseEvent(View.java:551) at com.sun.glass.ui.View.notifyMouse(View.java:937) at com.sun.glass.ui.mac.MacView.notifyMouse(MacView.java:127)

[diazandr3s]

Hi @Mena-SA-Kamel,

Thanks for opening this discussion.

The current MONAI Label + QuPath implementation requires both server and client to be on the same PC. Transferring histopathological images from the server to the client will take a significant amount of time.

The host requires authentication via some credentials.

Do you mean the MONAI Label server? It shouldn't require this. Can you please post the MONAI Label logs?

[Mena-SA-Kamel]

Thank you for your clarification. I was under the impression you can have the client and server on different PCs. Is the only limitation the image transfer between the client and server? If so, can we use cloud storage to allow the images to be shared between the client and server if they were to rest on different machines? The QuPath MONAILabel extension documentation is not really clear on this.

For your reference, I currently have QuPath running locally on my laptop and I am running MonaiLabel server on a remote PC (different IP address and requires authentication via username and password)

Below are the Monai Label logs:
(monailabel-env) oneai@mk-monai-6945f98bff-fx5vh:~$ monailabel start_server --app apps/pathology --studies wsi_images --host 127.0.0.1 Using PYTHONPATH=/home/oneai: [2022-09-06 12:02:26,470] [5882] [MainThread] [INFO] (__main__:269) - USING:: app = /home/oneai/apps/pathology [2022-09-06 12:02:26,470] [5882] [MainThread] [INFO] (__main__:269) - USING:: studies = /home/oneai/wsi_images [2022-09-06 12:02:26,470] [5882] [MainThread] [INFO] (__main__:269) - USING:: verbose = INFO [2022-09-06 12:02:26,470] [5882] [MainThread] [INFO] (__main__:269) - USING:: conf = None [2022-09-06 12:02:26,471] [5882] [MainThread] [INFO] (__main__:269) - USING:: host = 127.0.0.1 [2022-09-06 12:02:26,471] [5882] [MainThread] [INFO] (__main__:269) - USING:: port = 8000 [2022-09-06 12:02:26,471] [5882] [MainThread] [INFO] (__main__:269) - USING:: uvicorn_app = monailabel.app:app [2022-09-06 12:02:26,471] [5882] [MainThread] [INFO] (__main__:269) - USING:: ssl_keyfile = None [2022-09-06 12:02:26,471] [5882] [MainThread] [INFO] (__main__:269) - USING:: ssl_certfile = None [2022-09-06 12:02:26,471] [5882] [MainThread] [INFO] (__main__:269) - USING:: ssl_keyfile_password = None [2022-09-06 12:02:26,471] [5882] [MainThread] [INFO] (__main__:269) - USING:: ssl_ca_certs = None [2022-09-06 12:02:26,471] [5882] [MainThread] [INFO] (__main__:269) - USING:: workers = None [2022-09-06 12:02:26,471] [5882] [MainThread] [INFO] (__main__:269) - USING:: limit_concurrency = None [2022-09-06 12:02:26,471] [5882] [MainThread] [INFO] (__main__:269) - USING:: access_log = False [2022-09-06 12:02:26,471] [5882] [MainThread] [INFO] (__main__:269) - USING:: log_config = None [2022-09-06 12:02:26,471] [5882] [MainThread] [INFO] (__main__:269) - USING:: dryrun = False [2022-09-06 12:02:26,471] [5882] [MainThread] [INFO] (__main__:269) - USING:: action = start_server [2022-09-06 12:02:26,471] [5882] [MainThread] [INFO] (__main__:273) - ENV SETTINGS:: MONAI_LABEL_API_STR = [2022-09-06 12:02:26,471] [5882] [MainThread] [INFO] (__main__:273) - ENV SETTINGS:: MONAI_LABEL_PROJECT_NAME = MONAILabel [2022-09-06 12:02:26,471] [5882] [MainThread] [INFO] (__main__:273) - ENV SETTINGS:: MONAI_LABEL_APP_DIR = /home/oneai/apps/pathology [2022-09-06 12:02:26,471] [5882] [MainThread] [INFO] (__main__:273) - ENV SETTINGS:: MONAI_LABEL_STUDIES = /home/oneai/wsi_images [2022-09-06 12:02:26,471] [5882] [MainThread] [INFO] (__main__:273) - ENV SETTINGS:: MONAI_LABEL_AUTH_ENABLE = False [2022-09-06 12:02:26,471] [5882] [MainThread] [INFO] (__main__:273) - ENV SETTINGS:: MONAI_LABEL_AUTH_DB = [2022-09-06 12:02:26,472] [5882] [MainThread] [INFO] (__main__:273) - ENV SETTINGS:: MONAI_LABEL_APP_CONF = '{}' [2022-09-06 12:02:26,472] [5882] [MainThread] [INFO] (__main__:273) - ENV SETTINGS:: MONAI_LABEL_TASKS_TRAIN = True [2022-09-06 12:02:26,472] [5882] [MainThread] [INFO] (__main__:273) - ENV SETTINGS:: MONAI_LABEL_TASKS_STRATEGY = True [2022-09-06 12:02:26,472] [5882] [MainThread] [INFO] (__main__:273) - ENV SETTINGS:: MONAI_LABEL_TASKS_SCORING = True [2022-09-06 12:02:26,472] [5882] [MainThread] [INFO] (__main__:273) - ENV SETTINGS:: MONAI_LABEL_TASKS_BATCH_INFER = True [2022-09-06 12:02:26,472] [5882] [MainThread] [INFO] (__main__:273) - ENV SETTINGS:: MONAI_LABEL_DATASTORE = [2022-09-06 12:02:26,472] [5882] [MainThread] [INFO] (__main__:273) - ENV SETTINGS:: MONAI_LABEL_DATASTORE_USERNAME = [2022-09-06 12:02:26,472] [5882] [MainThread] [INFO] (__main__:273) - ENV SETTINGS:: MONAI_LABEL_DATASTORE_PASSWORD = [2022-09-06 12:02:26,472] [5882] [MainThread] [INFO] (__main__:273) - ENV SETTINGS:: MONAI_LABEL_DATASTORE_API_KEY = [2022-09-06 12:02:26,472] [5882] [MainThread] [INFO] (__main__:273) - ENV SETTINGS:: MONAI_LABEL_DATASTORE_CACHE_PATH = [2022-09-06 12:02:26,472] [5882] [MainThread] [INFO] (__main__:273) - ENV SETTINGS:: MONAI_LABEL_DATASTORE_PROJECT = [2022-09-06 12:02:26,472] [5882] [MainThread] [INFO] (__main__:273) - ENV SETTINGS:: MONAI_LABEL_DATASTORE_ASSET_PATH = [2022-09-06 12:02:26,472] [5882] [MainThread] [INFO] (__main__:273) - ENV SETTINGS:: MONAI_LABEL_DATASTORE_DSA_ANNOTATION_GROUPS = [2022-09-06 12:02:26,472] [5882] [MainThread] [INFO] (__main__:273) - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_USERNAME = [2022-09-06 12:02:26,472] [5882] [MainThread] [INFO] (__main__:273) - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_PASSWORD = [2022-09-06 12:02:26,472] [5882] [MainThread] [INFO] (__main__:273) - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_CACHE_PATH = [2022-09-06 12:02:26,472] [5882] [MainThread] [INFO] (__main__:273) - ENV SETTINGS:: MONAI_LABEL_QIDO_PREFIX = [2022-09-06 12:02:26,472] [5882] [MainThread] [INFO] (__main__:273) - ENV SETTINGS:: MONAI_LABEL_WADO_PREFIX = [2022-09-06 12:02:26,472] [5882] [MainThread] [INFO] (__main__:273) - ENV SETTINGS:: MONAI_LABEL_STOW_PREFIX = [2022-09-06 12:02:26,472] [5882] [MainThread] [INFO] (__main__:273) - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_FETCH_BY_FRAME = False [2022-09-06 12:02:26,472] [5882] [MainThread] [INFO] (__main__:273) - ENV SETTINGS:: MONAI_LABEL_DATASTORE_AUTO_RELOAD = True [2022-09-06 12:02:26,472] [5882] [MainThread] [INFO] (__main__:273) - ENV SETTINGS:: MONAI_LABEL_DATASTORE_FILE_EXT = '["*.nii.gz", "*.nii", "*.nrrd", "*.jpg", "*.png", "*.tif", "*.svs", "*.xml"]' [2022-09-06 12:02:26,473] [5882] [MainThread] [INFO] (__main__:273) - ENV SETTINGS:: MONAI_LABEL_SERVER_PORT = 8282 [2022-09-06 12:02:26,473] [5882] [MainThread] [INFO] (__main__:273) - ENV SETTINGS:: MONAI_LABEL_CORS_ORIGINS = '[]' [2022-09-06 12:02:26,473] [5882] [MainThread] [INFO] (__main__:273) - ENV SETTINGS:: MONAI_LABEL_SESSIONS = True [2022-09-06 12:02:26,473] [5882] [MainThread] [INFO] (__main__:273) - ENV SETTINGS:: MONAI_LABEL_SESSION_PATH = [2022-09-06 12:02:26,473] [5882] [MainThread] [INFO] (__main__:273) - ENV SETTINGS:: MONAI_LABEL_SESSION_EXPIRY = 3600 [2022-09-06 12:02:26,473] [5882] [MainThread] [INFO] (__main__:273) - ENV SETTINGS:: MONAI_LABEL_INFER_CONCURRENCY = -1 [2022-09-06 12:02:26,473] [5882] [MainThread] [INFO] (__main__:273) - ENV SETTINGS:: MONAI_LABEL_INFER_TIMEOUT = 600 [2022-09-06 12:02:26,473] [5882] [MainThread] [INFO] (__main__:273) - ENV SETTINGS:: MONAI_LABEL_AUTO_UPDATE_SCORING = True [2022-09-06 12:02:26,473] [5882] [MainThread] [INFO] (__main__:274) - Allow Origins: ['*'] [2022-09-06 12:02:26,948] [5882] [MainThread] [INFO] (uvicorn.error:75) - Started server process [5882] [2022-09-06 12:02:26,949] [5882] [MainThread] [INFO] (uvicorn.error:45) - Waiting for application startup. [2022-09-06 12:02:26,949] [5882] [MainThread] [INFO] (monailabel.interfaces.utils.app:38) - Initializing App from: /home/oneai/apps/pathology; studies: /home/oneai/wsi_images; conf: {} [2022-09-06 12:02:26,950] [5882] [MainThread] [INFO] (monailabel.utils.others.class_utils:36) - Subclass for MONAILabelApp Found: <class 'main.MyApp'> [2022-09-06 12:02:26,962] [5882] [MainThread] [INFO] (monailabel.utils.others.class_utils:36) - Subclass for TaskConfig Found: <class 'lib.configs.deepedit_nuclei.DeepEditNuclei'> [2022-09-06 12:02:26,963] [5882] [MainThread] [INFO] (monailabel.utils.others.class_utils:36) - Subclass for TaskConfig Found: <class 'lib.configs.nuclick.NuClick'> [2022-09-06 12:02:26,963] [5882] [MainThread] [INFO] (monailabel.utils.others.class_utils:36) - Subclass for TaskConfig Found: <class 'lib.configs.segmentation_nuclei.SegmentationNuclei'> [2022-09-06 12:02:26,964] [5882] [MainThread] [INFO] (main:77) - +++ Adding Model: deepedit_nuclei => lib.configs.deepedit_nuclei.DeepEditNuclei BasicUNet features: (32, 64, 128, 256, 512, 32). [2022-09-06 12:02:27,070] [5882] [MainThread] [INFO] (main:77) - +++ Adding Model: nuclick => lib.configs.nuclick.NuClick BasicUNet features: (32, 64, 128, 256, 512, 32). [2022-09-06 12:02:27,157] [5882] [MainThread] [INFO] (main:77) - +++ Adding Model: segmentation_nuclei => lib.configs.segmentation_nuclei.SegmentationNuclei BasicUNet features: (32, 64, 128, 256, 512, 32). [2022-09-06 12:02:27,249] [5882] [MainThread] [INFO] (main:81) - +++ Using Models: ['deepedit_nuclei', 'nuclick', 'segmentation_nuclei'] [2022-09-06 12:02:27,249] [5882] [MainThread] [INFO] (monailabel.interfaces.app:128) - Init Datastore for: /home/oneai/wsi_images [2022-09-06 12:02:27,249] [5882] [MainThread] [INFO] (monailabel.datastore.local:125) - Auto Reload: True; Extensions: ['*.nii.gz', '*.nii', '*.nrrd', '*.jpg', '*.png', '*.tif', '*.svs', '*.xml'] [2022-09-06 12:02:27,251] [5882] [MainThread] [INFO] (monailabel.datastore.local:540) - Invalidate count: 0 [2022-09-06 12:02:27,251] [5882] [MainThread] [INFO] (monailabel.datastore.local:145) - Start observing external modifications on datastore (AUTO RELOAD) [2022-09-06 12:02:27,252] [5882] [MainThread] [INFO] (lib.configs.deepedit_nuclei:60) - Using Preload: 0; ROI Size: [1024, 1024] [2022-09-06 12:02:27,252] [5882] [MainThread] [INFO] (main:122) - +++ Adding Inferer:: deepedit_nuclei => <lib.infers.deepedit_nuclei.DeepEditNuclei object at 0x7f635565ce50> [2022-09-06 12:02:27,253] [5882] [MainThread] [INFO] (main:122) - +++ Adding Inferer:: nuclick => <lib.infers.nuclick.NuClick object at 0x7f6353450700> [2022-09-06 12:02:27,253] [5882] [MainThread] [INFO] (lib.configs.segmentation_nuclei:72) - Using Preload: 0; ROI Size: [1024, 1024] [2022-09-06 12:02:27,253] [5882] [MainThread] [INFO] (main:122) - +++ Adding Inferer:: segmentation_nuclei => <lib.infers.segmentation_nuclei.SegmentationNuclei object at 0x7f6353450760> [2022-09-06 12:02:27,253] [5882] [MainThread] [INFO] (main:136) - +++ Adding Trainer:: deepedit_nuclei => <lib.trainers.deepedit_nuclei.DeepEditNuclei object at 0x7f63521dfe50> [2022-09-06 12:02:27,253] [5882] [MainThread] [INFO] (main:136) - +++ Adding Trainer:: nuclick => <lib.trainers.nuclick.NuClick object at 0x7f63521dfeb0> [2022-09-06 12:02:27,253] [5882] [MainThread] [INFO] (main:136) - +++ Adding Trainer:: segmentation_nuclei => <lib.trainers.segmentation_nuclei.SegmentationNuclei object at 0x7f63521dfe80> [2022-09-06 12:02:27,253] [5882] [MainThread] [INFO] (monailabel.utils.sessions:51) - Session Path: /home/oneai/.cache/monailabel/sessions [2022-09-06 12:02:27,254] [5882] [MainThread] [INFO] (monailabel.utils.sessions:52) - Session Expiry (max): 3600 [2022-09-06 12:02:27,254] [5882] [MainThread] [INFO] (monailabel.interfaces.app:460) - App Init - completed [2022-09-06 12:02:27,254] [timeloop] [INFO] Starting Timeloop.. [2022-09-06 12:02:27,254] [5882] [MainThread] [INFO] (timeloop:60) - Starting Timeloop.. [2022-09-06 12:02:27,254] [timeloop] [INFO] Registered job <function MONAILabelApp.on_init_complete.<locals>.run_scheduler at 0x7f635546eb80> [2022-09-06 12:02:27,254] [5882] [MainThread] [INFO] (timeloop:42) - Registered job <function MONAILabelApp.on_init_complete.<locals>.run_scheduler at 0x7f635546eb80> [2022-09-06 12:02:27,254] [timeloop] [INFO] Timeloop now started. Jobs will run based on the interval set [2022-09-06 12:02:27,254] [5882] [MainThread] [INFO] (timeloop:63) - Timeloop now started. Jobs will run based on the interval set [2022-09-06 12:02:27,255] [5882] [MainThread] [INFO] (uvicorn.error:59) - Application startup complete. [2022-09-06 12:02:27,255] [5882] [MainThread] [INFO] (uvicorn.error:206) - Uvicorn running on http://127.0.0.1:8000 (Press CTRL+C to quit)

[diazandr3s]

Thanks for the logs, @Mena-SA-Kamel. I don't see errors from those.

As histopathological images are quite heavy, transferring them from the server to the client can deteriorate the user experience. Here we tried to explain the current status of MONAI Label + QuPath: https://github.com/Project-MONAI/MONAILabel/tree/main/sample-apps/pathology#qupath

Open Sample Whole Slide Image in QuPath (which is shared as studies for MONAILabel server)

Both the server and client should share the folder where the studies are located.

Hope this makes sense :)

[Mena-SA-Kamel]

Thank you for clarifying. Is having QuPath connect to a remote MonaiLabel Server in the project scope? If not, is there a work around that we can use, for e.g. a shared synchronized cloud folder that is common between the two machines such as OneDrive/S3?

[SachidanandAlle]

QuPath was developed more of a prototype work.. We are still waiting for QuPath community to take it from here and contribute a full fledged plugin for everyone to use..

This is more of a reference implementation for small set of MONAILabel APIs..
What you are asking is all possible (including cloud support - cloud is shared between MONAILabel and QuPath..) but some work needs to be done on QuPath for that..

Otherwise due to better collaboration in our previous release cycle, we picked DSA as our main plugin to be part of Pathology use-case fo rmonailabel.

[SachidanandAlle]

And we do welcome any contributions that can help to enhance it further.. please feel free to contribute to MONAILabel in that direction.. it's a open source project :)