500 Internal Server Error

[PierreHNR]

Hello,

Thanks a lot for all your work! I followed the installation, but when I try to run Cellpose or Stardist algorythm, I get an "500 Internal Server Error" in Qupath. For your information, I am able to run SAM (even if I have a message that no GPU support is found) in Qupath thanks to your instructions.

Here is the full message in the command prompt:

(cellsparse-api) C:\Users\Pierre.HENER>uvicorn cellsparse_api.main:app
INFO: Started server process [20576]
INFO: Waiting for application startup.
INFO: Application startup complete.
INFO: Uvicorn running on http://127.0.0.1:8000 (Press CTRL+C to quit)
INFO: 127.0.0.1:63090 - "POST /sam/ HTTP/1.1" 404 Not Found
2023-06-23 16:40:42,473 [INFO] WRITING LOG OUTPUT TO C:\Users\Pierre.HENER.cellpose\run.log
INFO: 127.0.0.1:63098 - "POST /cellpose/ HTTP/1.1" 500 Internal Server Error
ERROR: Exception in ASGI application
Traceback (most recent call last):
File "C:\Users\Pierre.HENER\anaconda3\envs\cellsparse-api\lib\site-packages\uvicorn\protocols\http\httptools_impl.py", line 435, in run_asgi
result = await app( # type: ignore[func-returns-value]
File "C:\Users\Pierre.HENER\anaconda3\envs\cellsparse-api\lib\site-packages\uvicorn\middleware\proxy_headers.py", line 78, in call
return await self.app(scope, receive, send)
File "C:\Users\Pierre.HENER\anaconda3\envs\cellsparse-api\lib\site-packages\fastapi\applications.py", line 276, in call
await super().call(scope, receive, send)
File "C:\Users\Pierre.HENER\anaconda3\envs\cellsparse-api\lib\site-packages\starlette\applications.py", line 122, in call
await self.middleware_stack(scope, receive, send)
File "C:\Users\Pierre.HENER\anaconda3\envs\cellsparse-api\lib\site-packages\starlette\middleware\errors.py", line 184, in call
raise exc
File "C:\Users\Pierre.HENER\anaconda3\envs\cellsparse-api\lib\site-packages\starlette\middleware\errors.py", line 162, in call
await self.app(scope, receive, _send)
File "C:\Users\Pierre.HENER\anaconda3\envs\cellsparse-api\lib\site-packages\starlette\middleware\exceptions.py", line 79, in call
raise exc
File "C:\Users\Pierre.HENER\anaconda3\envs\cellsparse-api\lib\site-packages\starlette\middleware\exceptions.py", line 68, in call
await self.app(scope, receive, sender)
File "C:\Users\Pierre.HENER\anaconda3\envs\cellsparse-api\lib\site-packages\fastapi\middleware\asyncexitstack.py", line 21, in call
raise e
File "C:\Users\Pierre.HENER\anaconda3\envs\cellsparse-api\lib\site-packages\fastapi\middleware\asyncexitstack.py", line 18, in call
await self.app(scope, receive, send)
File "C:\Users\Pierre.HENER\anaconda3\envs\cellsparse-api\lib\site-packages\starlette\routing.py", line 718, in call
await route.handle(scope, receive, send)
File "C:\Users\Pierre.HENER\anaconda3\envs\cellsparse-api\lib\site-packages\starlette\routing.py", line 276, in handle
await self.app(scope, receive, send)
File "C:\Users\Pierre.HENER\anaconda3\envs\cellsparse-api\lib\site-packages\starlette\routing.py", line 66, in app
response = await func(request)
File "C:\Users\Pierre.HENER\anaconda3\envs\cellsparse-api\lib\site-packages\fastapi\routing.py", line 237, in app
raw_response = await run_endpoint_function(
File "C:\Users\Pierre.HENER\anaconda3\envs\cellsparse-api\lib\site-packages\fastapi\routing.py", line 163, in run_endpoint_function
return await dependant.call(**values)
File "C:\Users\Pierre.HENER\anaconda3\envs\cellsparse-api\lib\site-packages\cellsparse_api\main.py", line 175, in cellpose
return run(
File "C:\Users\Pierre.HENER\anaconda3\envs\cellsparse-api\lib\site-packages\cellsparse_api\main.py", line 42, in run
img = normalize(decode_image(b64img), 0, 100, axis=(0, 1))
File "C:\Users\Pierre.HENER\anaconda3\envs\cellsparse-api\lib\site-packages\cellsparse_api\main.py", line 30, in decode_image
return np.array(Image.open(io.BytesIO(base64.b64decode(b64data))))
File "C:\Users\Pierre.HENER\anaconda3\envs\cellsparse-api\lib\site-packages\PIL\Image.py", line 3298, in open
raise UnidentifiedImageError(msg)
PIL.UnidentifiedImageError: cannot identify image file <_io.BytesIO object at 0x000001FE10E2EE80>

Thank you!

[ksugar]

I think the error is the same one shown below.

Thank you @FabianaMoresi, for reporting the issue!
It seems that the error happened when it tried to decode the image.
If you use an image with multi-channels, this error may happen.
I will work on solving it as soon as possible and will let you know once it's done.
For the moment, only grayscale images will work properly. If you want to test how it works, please try it with the grayscale images.

Originally posted by @ksugar in ksugar/cellsparse-api#2 (comment)

I will work on solving it. Thanks.