segmentation of 3D data

[tischi]

Hello,

I was wondering whether cellPose also works on 3D data?
Specifically, we have 3D stacks with cells as shown below:

[tischi]

Wow. It works really well in 2D!
But 3D?

[VolkerH]

@tischi, have a look at #16

[carsen-stringer]

You can now drag-and-drop this 3D tiff into cellpose and the 3D version will run in the GUI, using the model you choose and the channels you set (Note: you will have to set the diameter manually)

See info on 3D format here

[tischi]

Great! I tried to upload this file onto the website but nothing happened. Could you please try as well?

[marius10p]

The website is only for 2D data. You need to install Cellpose on your computer for the 3D version.

[tischi]

Thank you!