QuPath_ TMA Annotations Question


I am a new QuPath user and was trying to find the answer online but couldn’t so thought of asking here. I am analyzing a set of TMA’s for 3 different markers and would liek to create 3 different projects for each marker. For the first marker, I modified the TMA dearrayer + applied to simple tissue detection and I would like to apply these same settings to the other two projects. I was not sure how to go about this … is there a way for me to export my current project annotations to a new project?

Would need more details to give a better answer.

I don’t even know if your markers are in the same image. Brightfield? Stripping and restaining?

Note that the Milestone versions have an option to align two different images and move objects between them.

There are simple scripts to export annotations to a file and reimport them.
*cleaned up the link.

How well these work may depend on which version of QuPath you are using.

Hello, thank you for your reply!

I am using Milestone 5 and my TMA has 3 stains (DAB, Teal, Purple + counterstain).
Attached is a picture of what it looks like (in the image below we only see DAB, Teal)

For this TMA, I performed the TMA dearrayer + simple tissue detection and have this so far with what I have adjusted.

Before I proceed with further analyses I want to be able to save these annotations and apply them to another project which has the same TMA scan to save time. The reason being, we will be using this TMA for diffferent projects in the lab and so I was wondering if there was a way to save the annotation so that in the future this could be applied to the section since the slide is the same. Hope this makes more sense

If the images are exactly the same (not the same slide, but the same image file), you can copy the qpdata file out of the data folder within your project, and place it into the new project. Solves that problem. The script I posted above should work as well, for the annotations, but you would still have to recreate the TMA, so I recommend going with the qpdata file. If you have one image in each project the file will be something like
Overwrite the data.qpdata file in the new project that has no annotations. Or, even more easily… just copy the project folder to a new location. No need to transfer at all.

That said, the staining looks reasonably clear and well separated, and you can probably classify and get cell counts within a single project with a decent spread of color vectors. If you are able to host a sample file, I could take a quick look.