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mahmoodlab / UNI

Towards a general-purpose foundation model for computational pathology - Nature Medicine
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ROI feature extraction #24

Closed rongyua closed 1 month ago

rongyua commented 6 months ago

Hello, thank you very much for your contribution. In your paper, you mentioned using the UNI pre-trained encoder to extract features from histopathology ROI, and also provided sample code. What I want to know is whether the ROI needs to be segmented in advance or not. Using the whole WSI image as input, if an image has multiple ROIs, can you provide me with a code example, I will be grateful

Richarizardd commented 1 month ago

Hi @rongyua - many ROI datasets such as CRC-100K should come as a zipped folder of ROIs (in an ImageFolder format), so the current code that has been made available in UNI should be sufficient for supporting most ROI datasets.

For WSIs, please see the updated CLAM codebase which supports WSI feature extraction for UNI/CONCH.