Is it possible to view only the positive cells in Positive Cell Detection?

Is it possible to get an image from QuPath with only the DAB positive cells as an overlay and then export it to ImageJ?
For example, an image of CD8+ or CD4+….etc?

This feels a bit like a rough answer and I suspect the answer might change if you explain why you want to do this but I would probably duplicate the image and data, use “Select Objects by Classifications” to select the Negative cells and then delete them. This would mean sending the region to ImageJ would have only the positive cells.


Hi @lmurphy,
Thanks so much for your reply.
I just wanted to see if it was possible to do to some analysis on the positively stained cells using ImageJ. Could you please tell me how I find the “Select Objects by Classifications” option? Is it on the latest version of QuPath (I’ve been using the old version so am uncertain if this version has this option).
Many Thanks!

It is in the context menu for any given classification on the Annotations tab.
Once you have done it, it should also show up in the Workflow to be used a a script line.

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For some reason it’s showing differently for me

It is on the latest version of QuPath.

For the old versions you would need to use a script to do something similar.
Something like.
removeObjects(getCellObjects().findAll{it.getPathClass() == getPathClass("Tumor")},true)

This will delete the objects without saving them, so you may need to reload your data to get the cells back.

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Thanks for that! I’ll play with the new version and see how I get on :slight_smile:

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