Two problems about size filter. Please help!

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Two problems about size filter. Please help!

Dear imagej-users


I have two problems about size filter. The content is a little long, but Please!!! Please look at it patiently. This problem has puzzled me for a long time…


1) Can someone help me to check my size filter workflow is right or not?


I want to give my segmentation result clean up.

my sample’s foreground is grains(i.e. soil), and the background is voids(i.e. pores).


I would like to remove the all isolated cluster grains in the background, so I used the Process- Binary-Fill hole to achieve this.

Then I invert the images to make the foreground is voids(because this is my final target to analysis), and the background is grains. Now I want to remove the void isolated cluster whose size is smaller than 10 voxels. I use the Plugin-BoneJ-Analyse Particles to set the size filter is 10 to do this.


This is my simple macro for your reference:

run(“Fill Holes”, “stack”);
run(“Invert”, “stack”);
run(“Particle Analyser”, “surface_area enclosed_volume moments euler thickness mask ellipsoids min=10.000 max=Infinity surface_resampling=2 show_particle show_surfaces show_centroids show_axes show_ellipsoids show_stack surface=Gradient split=0.000 volume_resampling=2”);


 I am a beginner in ImageJ, and I am afraid of some logical problems, so I would like to ask you to help me to have a look that the above idea is right? Or, do you have any better suggestions?


2) If the above operation is correct, then I will get the final size filter result from Plugin-BoneJ-Analyse Particles. But how can I transform this result images into an 8-bit images for the later analysis?


I tried Image > Adjust > Threshold to binarize the particle label image named like “XX_parts”, but the result is not good.  Because some details will be lost and cannot be binarized, that is to say, there is a loss of objects between binarized images and the original “XX_parts” images.


And I find it strange in Analyse Particles results that there are also differences between “XX_parts” image and “XX_volume” image. To be honest, I don't quite understand. I think both of them should be the same, just that one shows the label ID information and the other shows the volume information. So the idea that I want to use volume image to do binarization seems to be infeasible.

Does anyone know how to solve this?


Any kind of help will be greatly appreciated!


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Mengying Ni
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