QuPath Unsupported File Type

I have successfully downloaded Monai Label and QuPath. I had large .svs files and extracted regions of interest as .tif files. When trying out nuclei segmentation on those images, I got the following error:

The version_base parameter is not specified.
Please specify a compatability version level, or None.
Will assume defaults for version 1.1
[2024-12-16 12:58:42,829] [74427] [MainThread] [INFO] (main:175) - +++ Adding Trainer:: segmentation_nuclei => <lib.trainers.segmentation_nuclei.SegmentationNuclei object at 0x177fc7110>
[2024-12-16 12:58:42,830] [74427] [MainThread] [INFO] (main:196) - Active Learning Strategies:: ['wsi_random']
[2024-12-16 12:58:42,830] [74427] [MainThread] [INFO] (monailabel.utils.sessions:51) - Session Path: /Users/waldmanad/.cache/monailabel/sessions
[2024-12-16 12:58:42,830] [74427] [MainThread] [INFO] (monailabel.utils.sessions:52) - Session Expiry (max): 3600
[2024-12-16 12:58:42,830] [74427] [MainThread] [INFO] (monailabel.interfaces.app:469) - App Init - completed
[2024-12-16 12:58:42,830] [timeloop] [INFO] Starting Timeloop..
[2024-12-16 12:58:42,830] [timeloop] [INFO] Starting Timeloop..
[2024-12-16 12:58:42,830] [74427] [MainThread] [INFO] (timeloop:60) - Starting Timeloop..
[2024-12-16 12:58:42,830] [timeloop] [INFO] Registered job <function MONAILabelApp.on_init_complete..run_scheduler at 0x177e68c20>
[2024-12-16 12:58:42,830] [timeloop] [INFO] Registered job <function MONAILabelApp.on_init_complete..run_scheduler at 0x177e68c20>
[2024-12-16 12:58:42,830] [74427] [MainThread] [INFO] (timeloop:42) - Registered job <function MONAILabelApp.on_init_complete..run_scheduler at 0x177e68c20>
[2024-12-16 12:58:42,830] [timeloop] [INFO] Timeloop now started. Jobs will run based on the interval set
[2024-12-16 12:58:42,830] [timeloop] [INFO] Timeloop now started. Jobs will run based on the interval set
[2024-12-16 12:58:42,830] [74427] [MainThread] [INFO] (timeloop:63) - Timeloop now started. Jobs will run based on the interval set
[2024-12-16 12:58:42,830] [74427] [MainThread] [INFO] (uvicorn.error:62) - Application startup complete.
[2024-12-16 12:58:42,831] [74427] [MainThread] [INFO] (uvicorn.error:215) - Uvicorn running on http://0.0.0.0:8000 (Press CTRL+C to quit)
[2024-12-16 12:58:51,896] [74427] [MainThread] [INFO] (monailabel.endpoints.activelearning:44) - Active Learning Request: {'strategy': 'wsi_random', 'image': '', 'patch_size': [1024, 1024], 'image_size': [0, 0]}
[2024-12-16 12:58:51,897] [74427] [MainThread] [INFO] (monailabel.tasks.activelearning.random:47) - Random: Selected Image: MS073_SC_C_ACST_L_2; Weight: 1734371931
[2024-12-16 12:58:51,900] [74427] [MainThread] [INFO] (monailabel.endpoints.activelearning:60) - Next sample: {'id': 'MS073_SC_C_ACST_L_2', 'weight': 1734371931, 'path': '/Users/waldmanad/datasets/MS073_SC_C_ACST_L_2.tif', 'ts': 1734371662, 'name': 'MS073_SC_C_ACST_L_2.tif'}
[2024-12-16 12:59:11,000] [74427] [MainThread] [INFO] (monailabel.endpoints.wsi_infer:109) - WSI Infer Request: {'model': 'segmentation_nuclei', 'image': 'MS073_SC_C_ACST_L_2', 'output': 'asap', 'level': 0, 'location': [0, 0], 'size': [1433, 1072], 'tile_size': [1024, 1024], 'min_poly_area': 30, 'foreground': [], 'background': [], 'max_workers': 1}
[2024-12-16 12:59:11,005] [74427] [MainThread] [ERROR] (uvicorn.error:408) - Exception in ASGI application
Traceback (most recent call last):
File "/opt/anaconda3/envs/monai/lib/python3.11/site-packages/uvicorn/protocols/http/h11_impl.py", line 403, in run_asgi
result = await app( # type: ignore[func-returns-value]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/anaconda3/envs/monai/lib/python3.11/site-packages/uvicorn/middleware/proxy_headers.py", line 60, in call
return await self.app(scope, receive, send)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/anaconda3/envs/monai/lib/python3.11/site-packages/fastapi/applications.py", line 1054, in call
await super().call(scope, receive, send)
File "/opt/anaconda3/envs/monai/lib/python3.11/site-packages/starlette/applications.py", line 113, in call
await self.middleware_stack(scope, receive, send)
File "/opt/anaconda3/envs/monai/lib/python3.11/site-packages/starlette/middleware/errors.py", line 187, in call
raise exc
File "/opt/anaconda3/envs/monai/lib/python3.11/site-packages/starlette/middleware/errors.py", line 165, in call
await self.app(scope, receive, _send)
File "/opt/anaconda3/envs/monai/lib/python3.11/site-packages/starlette/middleware/cors.py", line 85, in call
await self.app(scope, receive, send)
File "/opt/anaconda3/envs/monai/lib/python3.11/site-packages/starlette/middleware/exceptions.py", line 62, in call
await wrap_app_handling_exceptions(self.app, conn)(scope, receive, send)
File "/opt/anaconda3/envs/monai/lib/python3.11/site-packages/starlette/_exception_handler.py", line 53, in wrapped_app
raise exc
File "/opt/anaconda3/envs/monai/lib/python3.11/site-packages/starlette/_exception_handler.py", line 42, in wrapped_app
await app(scope, receive, sender)
File "/opt/anaconda3/envs/monai/lib/python3.11/site-packages/starlette/routing.py", line 715, in call
await self.middleware_stack(scope, receive, send)
File "/opt/anaconda3/envs/monai/lib/python3.11/site-packages/starlette/routing.py", line 735, in app
await route.handle(scope, receive, send)
File "/opt/anaconda3/envs/monai/lib/python3.11/site-packages/starlette/routing.py", line 288, in handle
await self.app(scope, receive, send)
File "/opt/anaconda3/envs/monai/lib/python3.11/site-packages/starlette/routing.py", line 76, in app
await wrap_app_handling_exceptions(app, request)(scope, receive, send)
File "/opt/anaconda3/envs/monai/lib/python3.11/site-packages/starlette/_exception_handler.py", line 53, in wrapped_app
raise exc
File "/opt/anaconda3/envs/monai/lib/python3.11/site-packages/starlette/_exception_handler.py", line 42, in wrapped_app
await app(scope, receive, sender)
File "/opt/anaconda3/envs/monai/lib/python3.11/site-packages/starlette/routing.py", line 73, in app
response = await f(request)
^^^^^^^^^^^^^^^^
File "/opt/anaconda3/envs/monai/lib/python3.11/site-packages/fastapi/routing.py", line 301, in app
raw_response = await run_endpoint_function(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/anaconda3/envs/monai/lib/python3.11/site-packages/fastapi/routing.py", line 212, in run_endpoint_function
return await dependant.call(**values)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/anaconda3/envs/monai/lib/python3.11/site-packages/monailabel/endpoints/wsi_infer.py", line 132, in api_run_wsi_inference
return run_wsi_inference(background_tasks, model, image, session_id, None, wsi, output)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/anaconda3/envs/monai/lib/python3.11/site-packages/monailabel/endpoints/wsi_infer.py", line 111, in run_wsi_inference
result = instance.infer_wsi(request)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/anaconda3/envs/monai/lib/python3.11/site-packages/monailabel/interfaces/app.py", line 643, in infer_wsi
infer_tasks = create_infer_wsi_tasks(request, image)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/anaconda3/envs/monai/lib/python3.11/site-packages/monailabel/interfaces/utils/wsi.py", line 44, in create_infer_wsi_tasks
with openslide.OpenSlide(image) as slide:
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/anaconda3/envs/monai/lib/python3.11/site-packages/openslide/init.py", line 207, in init
self._osr = lowlevel.open(filename)
^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/anaconda3/envs/monai/lib/python3.11/site-packages/openslide/lowlevel.py", line 258, in _check_open
raise OpenSlideUnsupportedFormatError("Unsupported or missing image file")
openslide.lowlevel.OpenSlideUnsupportedFormatError: Unsupported or missing image file

Can I not perform the segmentation on my .tif images?

Start with monailabel/interfaces/utils/wsi.py and the wsi_infer.py call path shown in the traceback, focusing on the OpenSlide.OpenSlide input handling. Reproduce the failure with the reported .tif image and determine whether this TIFF should be accepted; done means the unsupported-or-missing-image failure is resolved or the supported input requirements are made clear.