Import annotations AND measurements via script (or generating measurements) (inter OS)

[lesolorzanov (Leslie Solorzano)]

Hello community.

We’ve been working with QuPath with several people and everyone uses a different OS. Linux, Mac and Windows. We have a project made on Windows that when opened in the Mac it doesn’t contain the annotations. Maybe it’s also a matter of having different QuPath versions. The windows is using 0.2.0 m12 and the mac is using 0.2.3, and the linux uses all.

So we manage to import the annotations which we managed via a script and a geo json as in my previous question

But now we need the measurements of those annotations.

The thing is that while I can export polygons and export measurements independently as two separate files, I have not been able to import them both.

So the questions become:

• Is there a function that allows me to call a measurement routine on my newly imported annotations?
• Is there a way to import annotations and their measurements at the same time? while working with different versions, so not relying on libraries that can only be used in one version only?

I hope I am not complicating my life too much, I just want to be able to use a project in a different computer, with the same annotations and measurements so that we can get different experts to annotate the same cells.

[petebankhead (Pete)]

@lesolorzanov

We have a project made on Windows that when opened in the Mac it doesn’t contain the annotations.

I don’t see any reason why it wouldn’t. What exactly happens?
Did you check the contents of View → Show log for any error messages?

@lesolorzanov

Maybe it’s also a matter of having different QuPath versions. The windows is using 0.2.0 m12 and the mac is using 0.2.3, and the linux uses all.

Is this really necessary? It sounds like a bad idea and I can’t see any benefits – especially since there’s nothing stopping you having multiple versions of QuPath installed on a single machine.

The first thing I’d try is updating Windows to use v0.2.3 and see if the project works there.

@lesolorzanov

So the questions become:

• Is there a function that allows me to call a measurement routine on my newly imported annotations?
• Is there a way to import annotations and their measurements at the same time? while working with different versions, so not relying on libraries that can only be used in one version only?

I don’t have an answer to these questions, because in general they shouldn’t be necessary. I’ve worked with projects between QuPath versions and operating systems lots of times (I’m pretty sure others have as well). So I think the priority should be to understand why that isn’t working for you.

Standardizing the version should help. I’m also not sure from your post where Linux fits in (can it read the annotations?).

[lesolorzanov (Leslie Solorzano)]

I see. Thanks for the reply. I understand things should work, the problem is I don’t have access to these computers easily, the experts have them and I have to meet with them and work in their computers to see what happens.

So what you say is that if I am in windows, and I open an image, find cells and get their measurements, I save the project and I open it in the mac, it should load everything the same way?

I will come back about the logs.

Thank you for your time.

[petebankhead (Pete)]

@lesolorzanov

So what you say is that if I am in windows, and I open an image, find cells and get their measurements, I save the project and I open it in the mac, it should load everything the same way?

Yes, with the only additional step that the paths to the images will need to be updated on the Mac:
https://qupath.readthedocs.io/en/latest/docs/tutorials/projects.html#fix-paths

I don’t recall any reason why v0.2.0-m12 may be incompatible with v0.2.3, but in general I really wouldn’t advise trying to mix versions like that – especially not using one of the milestone (i.e. unstable) versions, since many things may have changed.

For more details, see
https://qupath.readthedocs.io/en/latest/docs/intro/versions.html