3D data support

[federico-carrara]

Hi!
First of all, congrats, and thanks for your amazing effort in building this nice repo!

I am considering using it for a nuclei segmentation project. Specifically, I am interested in Stardist and Cellpose models.
However, before digging in, I gave a glimpse to some of the codebase and noticed that models and datasets might not be working for 3D data at the moment. I also didn't find any reference to this nor in the README, neither in the examples I went through.

Can you confirm this observation? If yes, are you planning to modify the code to support 3D? If so, where does it fall on your priority list?

Thank you so much and again huge congrats on your work :)

[okunator]

Hi,

Thanks for the compliments! And yes you're right, there is no support for 3D segmentation currently. For now, there are no immediate plans to add 3D segmentation, BUT, since I'm currently free from other duties and can work on this repo for a couple months I'll see if I can manage to add 3D support among all the other renovation I need to work on in this repo. 3D segmentation would definately be an enhancement and will be down the line at some point in the future.

[guidoputignano]

Dear @okunator,
firstly, I would like to thank you for your fantastic library.
Personally, I am highly interested in 3D cellular segmentation so I can use your library even further.
In this case, would there be the possibility of having at least a 3D segmentation using some tools such as Stardist?
Your work is fantastic