Batch analysis for mIHC

Hi, I have been using Qupath to do fluorescent mIHC analysis. I am interested in identifying single, double or triple positive cell populations in multiple mIHC images which we got from one slide/sample. How I can do the same analysis on the multiple mIHC images at same time or in one batch? I tried the method learned in the workshop. But it looks like that method works for HE or bright field but not for fluorescent. Any help will be appreciated.


I’m not sure exactly what method you’re referring to. Have you seen this?

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Thanks for your prompt reply.
Yes. I have been following your instructions online (option 1) working great for one mIHC image each time. But now I want to improve the efficiency to do multiple (such as 6 image) mIHC image analysis at one time. How can I do this?
By the way, I used InForm to do the same analysis before. All the images were exported from InForm.

If your images are all in the same project, and you’ve saved your classifiers, you just apply those classifiers to the ‘new’ images (after detecting the cells).

In v0.2.0-m12 the steps should also be properly logged, meaning that you can (semi)automatically generate a script/macro for batch processing:

However this is quite sensitive to the exact steps you do, and the order in which you do them. Often, scripts require a bit of cleaning up.

Thanks. It runs efficiently when I used saved classifier to the new inport images. I will try script later on.
I am still using Qupath m9. Do I need to switch to m12?

Lots of things should be better in m12. If you don’t have a strong reason to stay with m9 (e.g. you’re in the middle of a large project and need to keep the exact same version), I would update.

And then to the ‘stable’ version of v0.2.0 which is due soon.