3d image support

[bpavie]

Hi, the issue for 3d support is still open, but you mention last year that you will support 3d images, is that the case now ?

Best,
Benjamin

[sameeul]

Hi Benjamin,
We have added some 3D supports at the moment. The users can feed stack (in Z-axis) of 2D images and calculate 3D image features. We are actively working on adding more 3D image features at the moment. Our plan is to implement most of the common 3D feature calculation before the year ends.

We then plan to work on few other arrangements of 3D images (ome-zarr, multi-directory 3D tiff images, etc).

I am also curious to know what 3D features you are looking for and how to you arrange your 3D image data (single file, multiple 2D files etc.).

Best,
Samee

[pr4deepr]

3D features you are looking for and how to you arrange your 3D image data (single file, multiple 2D files etc.).

Extremely keen on the 3D features.
I am not coming from a screening angle, but mostly confocal/lightsheet data.
With microscopy data, the vendors usually have a monolithic file which as the complete image data in it (czi, lif files)
We programatically access it as numpy arrays and then process it downstream.
In terms of how we organize our 3D image data for microscopy, they are usually processed as:

• ZYX
• CZYX ; (C: channel)

Hopefully this is useful

Cheers
Pradeep