Porosity analysis on image J- Should include holes be checked or unchecked?

[Shreyakanakiya]

Hello,

I want to perform porosity calculation on a CT scan image sequence of a rock. I have thresholded the images such that the pores are represented by black and non pores by the color white. When I use analyze particles without including holes, I get a porosity of about 69%. Whereas when I perform it by including holes, I get a porosity of 38%. I'm a little confused on what exactly the include holes function does. Since the pore spaces are essentially empty spaces/holes should I be using include holes function or not for accurate porosity calculation ?

Kindly help me out.Thank You very much in advance.

[Michael Doube-4]

Hi Shreyakanakiya,

> I want to perform porosity calculation on a CT scan image sequence of a
> rock.

Have you tried Volume Fraction and Analyse Particles in BoneJ? you might
find that 3D analysis better suits your 3D images.

http://bonej.org/volumefraction
http://bonej.org/particles

A few people have done soil and rock work with it, despite its name.

https://scholar.google.com/scholar?start=20&q=soil+OR+rock&hl=en&as_sdt=0,5&sciodt=0,5&cites=16814410598979768336&scipsc=1

Michael

 I have thresholded the images such that the pores are represented by

> black and non pores by the color white. When I use analyze particles
> *without including holes*, I get a porosity of about 69%. Whereas when I
> perform it by *including holes*, I get a porosity of 38%. I'm a little
> confused on what exactly the include holes function does. Since the pore
> spaces are essentially empty spaces/holes should I be using include holes
> function or not for accurate porosity calculation ?
>
> Kindly help me out.Thank You very much in advance.
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/Porosity-analysis-on-image-J-Should-include-holes-be-checked-or-unchecked-tp5013634.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
Michael Doube
BPhil BVSc PGCert(Vet Ed) PhD FHEA MRCVS
Lecturer, Comparative Biomedical Sciences
The Royal Veterinary College, University of London
London NW1 0TU
United Kingdom

[phone] (Internal: 5503)
@mdoube
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[Shreyakanakiya]

Hi Michael,

Thank you for your reply. I have been trying to use 3D viewer and BoneJ particle analyser. However, ImageJ stops working when I try to open images in 3D by volume rendering. My CT scan data is 3.5GB per sample so I even tried resampling it, however, it did not work. I am currently using an Intel(R) Core(TM) i5-4670 CPU 3.4ghz processor with 8GB RAM. Is the problem resulting because my computer doesn't have enough processing power or could there be some other reason ?
Thanks once again.

Regards,
Shreya

[Michael Doube-4]

Hi Shreya,

> Thank you for your reply. I have been trying to use 3D viewer and BoneJ
> particle analyser.

You don't need to open the data in the 3D viewer for BoneJ's analysis to run and give you a result. Since your images are so big, I'd suggest turning off the 3D rendering options in BoneJ's Particle Analyser.

> However, ImageJ stops working when I try to open images
> in 3D by volume rendering.

Experience shows that ImageJ's 3D viewer prefers small volumes, and as far as I'm aware is strongly constrained by the amount of video RAM on your graphics card. So you need a big card (with some GB of VRAM) to open that much data, even with resampling. You can try cropping out empty space and resampling the stack prior to trying to load in the 3D viewer.

> My CT scan data is 3.5GB per sample so I even
> tried resampling it, however, it did not work. I am currently using an
> Intel(R) Core(TM) i5-4670 CPU 3.4ghz processor with 8GB RAM. Is the problem
> resulting because my computer doesn't have enough processing power or could
> there be some other reason ?

Best regards,

Michael


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This message, together with any attachments, is intended for the stated addressee(s) only and may contain privileged or confidential information. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Royal Veterinary College.

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[Shreyakanakiya]

Hi Michael,
Thank you for the help.
Regards,
Shreya