CLAM config for HunCRC slide data

[anhtienng]

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Hello authors,

Thank you for you amazing work. Can you publish the config of CLAM for extracting HunCRC data ?

I can't extract, even with very low thresholds. {'seg_params': {'seg_level': -1, 'sthresh': 1, 'mthresh': 1, 'close': 4, 'use_otsu': True, 'keep_ids': 'none', 'exclude_ids': 'none'}, 'filter_params': {'a_t': 1, 'a_h': 1, 'max_n_holes': 10}, 'patch_params': {'use_padding': True, 'contour_fn': 'four_pt'}, 'vis_params': {'vis_level': -1, 'line_thickness': 50}}

Thank you.

[guillaumejaume]

What kind of tissue segmentation are you facing with HunCRC?

[Richarizardd]

Hi @anhtienng - closing this thread due to inactivity, but I will comment that the base CLAM configuration (tcga.csv) should be sufficient in processing HunCRC slides. Let me know if there are any issues.