Cortical Porosity

Dear BoneJ users,

I was wondering if anyone can help me to use ‘Volume Fraction’ on cortical bone image to estimate the cortical porosity. I would like to obtain the fraction of the sample that is pores. Has anyone tried to calculate cortical porosity using Po.V/Ct.V? Thanks in advanced for your help.

best regards

In principle this should be straightforward: you measure the volume fraction of the cortical bone having thresholded so that pores are distinct entities. You may need to spend a bit of effort defining ROIs and adding them to the ROI Manager, however. The ROI Interpolator may help you with that. Then tell Volume Fraction to limit to ROI Manager. The result will be reported as BV/TV - this is just a label on top of a measurement which is simply proportion of the volume that is foreground. To get the proportion of volume that is background, use 1 - BV/TV.

where do you find the "The ROI Interpolator "

This topic has the bonej tag, so I’d assume it is part of BoneJ.

And indeed, that’s the case:

Note that there’s also a version built into core ImageJ’s ROI Manager, that’s accessible via More > Interpolate ROIs (ij.plugin.RoiInterpolator).
I didn’t test how the two interpolators compare, as they are both authored by @mdoube, but (looking at the source code) seem to differ a bit.


The ROI Interpolator in ImageJ1 is I think pretty much copied out of BoneJ with some cosmetic changes that @Wayne made to the wrapper code. Also - I can’t claim credit, it was a joint effort with Johannes Schindelin who wrote the code that does the heavy lifting - I just wrapped it up a bit for ROI morphing. Brief docs on the BoneJ version are here.


Before I forget, you may benefit from getting used to drawing annular ROIs - that is, ROIs with holes cut out of the middle (which in your case are the medullary cavity).


Many thanks everyone. I will have a try and hope it works!

Dear all,

I’ve been trying the above protocols and get some results. I drew the ROI (pores) and added it to the ROI manager. I told the Volume Fraction to use the ROI manager. One the results I got BV/TV= 0.544. This is the foreground (pores). To get the background (Ct.V) 1-0.544= 0.456.

I’m not sure the results are correct? because the BV/TV of the pores is higher than the background.

Thannks in advance.


That’s not at all a surprising result, provided that your bone is about 55:45 pore:matrix. You haven’t told us much about the bones you are studying or the imaging technique, so the number is a bit tricky to interpret.

My only concern is that you may have (despite best efforts) included the medullary canal in your measurements.

1 Like