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bowang-lab / MedSAM

Segment Anything in Medical Images
https://www.nature.com/articles/s41467-024-44824-z
Apache License 2.0
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How to process pathological images? #325

Closed Leelinw closed 3 weeks ago

Leelinw commented 1 month ago

Hello! Thank you for your wonderful work！I want to know what to do when I need to process a large scale pathology image. I ran gui.py and circled the required section, but it identified the normal cells and ignored the cells I needed the label for. What's more, I need to circle plenty of times on the images since it's scale. I wonder if I need to get patches and then splice them together. image Thank you for your effort again！

JunMa11 commented 1 month ago

Hi @Leelinw ,

What is your segmentation target? If it is the gland, you may need to cut the WSI into patches before feeding it to medsam.

Leelinw commented 1 month ago

Hi @Leelinw ,

What is your segmentation target? If it is the gland, you may need to cut the WSI into patches before feeding it to medsam.

Thank you so much for your reply! What you said really makes sense, I'll try to cut my WSI and reprocessing them. Best Wishes!