Pore size analyses

I have following thresholded image of a soil slice which shows only the pores. I want to filter all the pores which are smaller than certain diameter (ECD) and visualize only the bigger pores. Can anyone help me with this…!thresholded1 before%20thresholding|468x450

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If you used Analyze->Analyze particles, there is an option to set the size threshold. Not sure if your image has pixels size metadata, so it may require some trial and error.

@Research_Associate Thank you!
Analyze particles option helped me to calculate the thresholded pores( size > 0.44 mm^2 in my case) but at the same time I also want to remove those smaller particles from my image so that I can visualize only the bigger pores in 3D.

Right, use the threshold for the size in Analyze particles.
It sounds like you don’t want to start at zero.
*You will want to generate a new binary image once you are done with that step.
Or during that step, actually.
Play around with the possible steps, I’m not that great with FIJI.


Appreciate that sir. But none of those options are helping me to get a new filtered image

I think the strategy suggested by @Research_Associate does help you do this? Unless we are both not understanding what you want to do from the details you’ve given us. If you re-do Analyze particles on that image you have the resultant mask image that @Research_Associate showed you how to get will have only the particles that meet the threshold you set.

Here’s an example I’ve done using the below macro code.
You can see that the resultant mask image ten has only the particles that meet the size threshold I set.

run("Blobs (25K)");
run("Convert to Mask");
run("Analyze Particles...", "size=500-Infinity show=Masks");
selectWindow("Mask of blobs.gif");
run("Invert LUT");

However, I noted that you originally asked about diameter which you might prefer compared to the Area measurement in Analyze Particles. So I suggest you look at the Extended Particle Analayzer that’s part of BioVoxxel (you might need to add thatUpdate site if you don’t already have it). It lets you filter particles based on a lot more measurements include Ferets diameters and also lets you output a mask image.

Does that help?


Thank you all. It worked. It was my bad. I inverted my image before analyzing the particle because of which I was not getting the required result.

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Does BioVoxxel> Extended particle analyzer work with image stacks? I think not.

I think the BioVoxxel suggestion was intended to give you more thresholding options. It would work as well as Analyze particles on a stack, I would guess.

Since I am more interested in thresholding the pores based on Equivalent Cylindrical Diameter (ECD) rather than the Ferret’s diameter that ImageJ basically uses, I am looking for better option than thresholding based on Area under the Particle Analysis.

BioVoxxel>extended particle analyzer didn’t work for my image stacks.

Hi @Suman56,

Sorry, I didn’t realise the EDM doesn’t work on stacks. It is, however, macro recordable so would be able to be included in a macro to run over multiple images in a stack if it was giving you preferable filering to the native Analyze Particles option.

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Please excuse my interruption, however the analysis in measurements allow the option of both major and minor Ferret diameters with the minor equivalent to the ECD you mention.

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@lmurphy thank you so much. that will surely help

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Thanks @smith_robertj . I can get the major and minor Ferret diameters from the analyses but I need my result all based upon ECD. I think that might help to get some idea though.