Open TingTingShao opened 4 months ago
what organ is the tissue from?
Liver
I can send one example image to you if that's better. BTW, is there a Discord channel for WSInfer?
Thanks, tingting
the main reason is that the tumor model you are using was trained on breast tissue. there's no guarantee that it would work well in liver, and i wouldn't expect it to work.
a solution would be to find a patch classification model for liver tumor. another option is to try qupath's built-in patch classification methods. if you opt to make your own liver tumor classifier, take a look at patch sorter https://github.com/choosehappy/PatchSorter
we don't have a discord server. most of the communication happens here in the github issues, sometimes in email.
Many thanks for your reply.
Quick response to your first point:
the main reason is that the tumor model you are using was trained on breast tissue. there's no guarantee that it would work well in liver, and i wouldn't expect it to work.
This is the breast cancer metastate in liver. In this case, I should also use the model in Liver? Do you have a specific model in your mind for me to choose?
Thanks for other suggestions, I am gonna explore later.
Thanks, tingting
This is the breast cancer metastate in liver. In this case, I should also use the model in Liver? Do you have a specific model in your mind for me to choose?
ah i see. this is a good question. patch classification models can be finicky, so i think the best solution would be to have a patch classifier trained on breast metastases in liver tissue. from your screenshot, it looks like the breast tumor model is applying false positives in the hepatocytes.
Dear,
This is my first try with WSInfer, and I would like to ask for more features and advice on it.
The aim of the project: (1) to identify metastasis sets, the statistics include: the number of the metastasis sets, and the area of each metastasis set. (2) To automate the process, as it took so long with manual annotation.
I tried with SAM extension, it works great with
Prompt
, but can not perform good withAuto mask
.I tried with WSInfer annotation to see if it can help with the automation, but I can clearly see that the results are not ideal though it was fast. The metastasis sets were labeled with low probability of tumor. The model I used was breast-tumor-renet34.
The images are as follows:
Any idea on how to improve this?
Looking forward to your reply. Thanks, tingting