3D

[Ju]

HI,

Im a university student and i'm new to imageJ. For one of my major work, I need to use imageJ to construct a 3D pore stucture of a sandstone sample such as ars.els-cdn.com/content/image/1-s2.0-S0167198712000931-gr1.jpg I have already threshold about 300 slice of the CT-scan images. Is it possible to guide me on how to do it? tried putting them into stacks and using 3d-project to come up with something but it doesn't look similar at all.

Thanks!

[Michael Doube-4]

Hi Julian

First of all, import your microtomography slice images as a series to make an image stack.

File>Import>Image Sequence...

Then binarize it by picking a threshold. The threshold can be applied to all the slices.

Image>Adjust>Threshold
(I guess you have strong contrast between sandstone matrix and background, which is e.g. water or air)

Then try running Purify, then Connectivity:
http://bonej.org/purify
http://bonej.org/connectivity

Your rock structure might be like trabecular bone, in which there is a single connected network of struts. Or else it might have disconnected particles or pore spaces. If there are several particles / pore spaces then use BoneJ's particle analyser I mentioned before which will tell you the Euler characteristic of each particle.

Connectivity is calculated from the Euler characteristic and assumes a single particle with no cavities is in the image. Connectivity can be interpreted as the number of connected branches in a structure. Connectivity density is just that divided by the volume of your sample.

Don't bother with 3D Project - that will make a 2D image from your 3D data.

Michael

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<http://imagej.1557.n6.nabble.com/file/n5001765/Sandstone-A_XY_000.jpg>
HI,

Im a university student and i'm new to imageJ. For one of my major work, I
need to use imageJ to construct a 3D pore stucture of a sandstone sample
such as ars.els-cdn.com/content/image/1-s2.0-S0167198712000931-gr1.jpg I
have already threshold about 300 slice of the CT-scan images. Is it possible
to guide me on how to do it? tried putting them into stacks and using
3d-project to come up with something but it doesn't look similar at all.

Thanks!

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