3D model without stacks

Hi, I’m pretty new to imageJ and image analysis in general but I have a question that I cannot seem to find a clear answer to which is the following:

I would like to construct a 3D model of a plant’s root system by taking side views (and potentially a top view) images. For obvious reasons, I cannot create a stack of slices along the vertical axis. Is this possible?

For example, I could create a setup where the plant is at a fixed position from the camera (with naked and clean roots hanging in the air). I could then rotate the plant 360 degrees in increments of 10 degrees, so 35 pictures in total.

Is ImageJ capable of rendering a 3D model of this root system?

Thank you.

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Hey @BananaBoy,

I’m not aware of an ImageJ-Plugin doing this. But you might want to read about tomographic reconstruction: https://en.m.wikipedia.org/wiki/Tomographic_reconstruction

Or did you already by chance?

I hope that helps.


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thanks for the quick help and reply. Also big thanks to Herbie who responded via e-mail and also suggested tomographic reconstruction. As it turns out, that will not work either, so I will have to look for some other way to model my root system. I might just go with a 2D image and using thresholding as good as I can to extract the variables that I need.

thanks again!

You might evaluate photogrammetry, too.

I don’t think that the resolution is high enough at the moment (at least for fine roots).

However, here a paper I found:

Here you find some software links:

See also:

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Hello there,
Have you already make a rotated version of what you wish?, and is the upper part of the plant necessary for your analysis?
Send any attempts you have already done and we can have a look at it.
There are a lot of ways to do things.

Thanks for all the great responses everyone. I’m new to this forum but am already blown away by the commitment in this community.
I hadn’t heard of photgrammetry but I will look into it for sure.

Bob, do you mean if I have taking the side view pictures yet? No, not yet. Also, the upper part is not necessary in the analysis of the roots. This part is being imaged twice a week while they are still in the experiment.

For now I was only hypothesizing. Basicly, the goal is phenotyping of root traits to drought tolerance for different banana wild relatives. I’m currently exploring image analysis as an option to speed up this process and automate it (as I’m dealing with a lot of plants). Up to now I’m using an overhead picture of the root system laid down side ways on a contrasting background in order to use thresholding and something like SmartRoot (a plugin for ImageJ). The 3D model would have been very interesting to include but is not absolutely necessary.

Thanks again!

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The point I was wondering was do you need the plant alive, and I guess you do. But if you can get rotated images as alighned as possible we may be able to accomplish some thing similar to 3D. Worth a try.

The paper Detailed Reconstruction of 3D Plant Root Shape seems relevant.

If you want to measure roots also consider to use the following tools not only relevant for root analysis:


Also search this forum and the ImageJ mailing list (older archive) for root analysis and similar.
You will find a lot of solutions and ideas far beyond specialized plugins.