Apologies if this is a very basic question but I am new to bone image processing (honours student). I am wanting to measure trabecular bone thickness and spacing using histology slides (so 2D images). My supervisor has previously used BoneJ to do this, and appears to still be able to. However, when I have tried to process a couple test images (training before I have my slides) BoneJ asks me for a 3D image.
I have tried finding a Legacy copy, as from my searches it seems things may have been updated since my supervisor stated using hit but I haven’t had a lot of luck.
I’d appreciated any suggestions as to how I might be able to use BoneJ for trabecular histomorphometric measurements.
For 2D measurements of thickness, use the inbuilt version of Local Thickness (use the search field in the taskbar or hit the [L] key and search), which should run on your 2D images by fitting circles rather than spheres.
BoneJ uses the inbuilt version of Local Thickness and adds some labelling and display sugar, but is basically the same. Take care that the units of the output make sense: they might be reported in pixels rather than as calibrated distances.
Thanks for replying. I have been able to process the image but the results don’t seem to be showing. Also, is there a away to do the trabecular spacing as well?
The “results” are the labelled image pixel values. Get the image statistics with the measure or histogram commands.
Invert the binary input image and run Local Thickness again.
Is there a way to change the result to report in the correct scale instead of in pixels?
Find out the pixel spacing with Image > Properties, then multiply your thicknesses (in pixels) by this value.