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mahmoodlab / CLAM

Data-efficient and weakly supervised computational pathology on whole slide images - Nature Biomedical Engineering
http://clam.mahmoodlab.org
GNU General Public License v3.0
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Pen Marking of Slides handled by CLAM #157

Closed shubhaminnani closed 2 years ago

shubhaminnani commented 2 years ago

Hi @fedshyvana Do CLAM handle the penn marked slides while segmenting ? Dont have any mask for tissue. So whatever CLAM is doing is their a way to tackle penn marking?

Thanks!

fedshyvana commented 2 years ago

Penmarks are not handled unfortunately - although for what it's worth if your goal is to simply train a classifier, we've found that the model is able to ignore the penmarkings and focus on tissue regions via attention. Although if your goal is perform other types of analysis then this could become an issue.

shubhaminnani commented 2 years ago

Thank you for your quick response. Attention is received by pen markings even though it is training a classifier. Will need to include a pre-processing seems to be.