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can I use CellViT to process tif files without metadata? #76

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xyz202310 opened this issue Nov 28, 2024 · 2 comments
Open

can I use CellViT to process tif files without metadata? #76

xyz202310 opened this issue Nov 28, 2024 · 2 comments

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@xyz202310
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Hi, thanks for this great tool!
I need to segment cell nucleus in H&E images. But the files are .tif format, and they have no additional information. Can I use CellViT to process these files?
Thank you!
@FabianHoerst
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Hi,

you could use the --wsi_propertiestag during preprocessing to hand over the magnification and mpp of the slide.

@FabianHoerst
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Take a closer look here: https://github.com/TIO-IKIM/CellViT/blob/main/docs/readmes/preprocessing.md#wsi-properties-dictionary

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@FabianHoerst @xyz202310