Volume Reconstruction from microCT stacks

[dence]

Hi, I have a very a general question about plantCV. Does plantCV currently have capabilities to identify features and estimate diameter and volume of features in microCT stacks? Is that the kind that could be added to plantCV or is that outside its scope?

Sorry if this is not the right place to ask the question.

Regards,
Daniel Ence

[nfahlgren]

Hi @dence!

We do not currently have any built-in methods for working with volumetric 3D data, but that would definitely be cool! If I understand correctly, would this be a stack of 2D images that a 3D shape could be built from and measured?

[dence]

That's correct. My PI uses microCT to identify and quantify features in wood microcores, but the current methods are either slow and laborious or limited by license issues at our campus compute cluster.

Here is one image from a stack. It has already been gray-scale converted which part of the current method.

[dschneiderch]

This seems more likely to come from the root world. @nfahlgren wasn't someone presenting on this at nappn?

[nfahlgren]

For sure, Ni Jiang from Chris Topp's group talked at the NAPPN meeting. Here's a couple of their recent preprints on x-ray CT and x-ray microscopy:

• https://www.biorxiv.org/content/10.1101/2021.03.03.433776v2
• https://www.biorxiv.org/content/10.1101/2020.12.18.423480v2

Plus groups at Michigan State, University of Nottingham, Fraunhofer, University of Adelaide, etc.

I definitely don't want to reinvent the wheel but I haven't seen publicly available software in this space yet (could be wrong of course!).

[dence]

Thank you for those resources. I'm tagging the PhD student working on the project (@mallorymaynes). I need to do thorough literature and software search but it seemed like something that would be possible with plantcv, especially given the modular architecture of the software.

Thanks,
Daniel