error trying to import .tif

[Jeatable]

When I try to import tif I get "ERROR [26500] FAST exception caught in Qt event handler OpenSlide was unable to open the file:...". The images from FastPathology Test project open without any error. My files are about 180 MB, and names are pretty long with dashes and underscores, so I tried renaming my tif to A01.tif and A01.tiff, and tried random 27 kB tif, resulting in the same error. I was able to process my tif with long filename in QuPath and MIB. Am I missing something, or should I post as issue?

[andreped]

Hello, @Jeatable! :]

Hard for me to say what the problem is within more details into what image you are attempting to use.

FastPathology only supports pyramidal images. If you attempt to open a regular non-pyramidal TIFF, it will not be able to render it. FastPathology was developed to render WSIs, not smaller regions only which may be stored as non-pyramidal image formats (e.g., PNG).

The reason why QuPath opens non-pyramidal images, is because it pyramidizes the image, if it is not already pyramidal - this can be very slow for larger WSIs.

I would assume you are trying to visualize non-pyramidal TIFFs?

[Jeatable]

No, it lets you directly save to .tif or .png. Even z-stacks are directly saved to these formats.

[andreped]

Oh, that's unfortunate and a bit surprising tbh...

Anyways, to install vips on Windows see here.

[Jeatable]

Using vips to generate a pyramidal tiff worked, also solved the 'imported but not being able to view' problem.

Now I'm trying to apply an .onnx model. Initially placed it in the /fastpathology/models folder but didn't find a possiblity to apply it in FASTPathology.

So I downloaded one of the existing colon HE models, and mimicked its structure. Created a title-model and title-fp folder in datahub folder, placed my .onnx file in the title-model folder and changed PipelineName, Attribute classes and Attribute model in the colon HE pipeline.fpl file and saved it to the new title-fp folder.

Two warnings in fastpahtology but it seems to be running,
WARNING [16048] Requested magnification level does not exist in image pyramid. Will now try to sample from a lower level and resize. This may increase runtime.
WARNING [16048] Patch size must be a multiple of 16 (TIFF limitation). Adding some overlap (32, 32) to fix.

However it has been running for over 3 hours, with the progress bar still at 0%. Is this normal during auto-tuning, or should I edit the .fpl file to prevent the warnings?

[andreped]

@Jeatable Could you open a new issue or discussion about this? Makes it easier for me and others to track different threads :]

I think I know what the issue is, but lets take it in a separate issue/discussion.

[Jeatable]

Will do!

Thanks for your help!