BoneJ not completing calculating Trabecular spacing causing CPU to run at 100%


I am trying to calculate the trabecular spacing and thickness on a raw image set that I have imported. After converting the set from 16bit to 8bit, when I run BoneJ Thickness calculator for both (spacing and thickness), the program will start and then just never complete. After a while my CPU will start to rev and show that its running at 100%. I narrowed this down to it getting stuck on calculating the spacing (thickness seems to work fine on its own)

Analysis goals

  • Trabecular Thickness, Trabecular Spacing & their mask images.

That’s exactly correct, except it’s not stuck, it’s just trying to fit spheres to the background of your input image which might not be well-bounded. Think of the algorithm as blowing up bubbles until the bubble touches something then pops. If the object is in the middle of the image surrounded by background, what happens is that the background ‘bubbles’ grow and grow and never touch the sides. The algorithm assumes that outside your image is also background. So, you need somehow to stop those huge background bubbles from forming: either by filling it with foreground (after calculating thickness) or by drawing a box of foreground to stop the background bubbles from growing. Note that all of the algorithms in BoneJ are stupid: they know nothing about anything apart from pixels and basic geometry - they don’t know what your sample is, where it is, what should be counted and what shouldn’t be counted, until you tell them explicitly with your foreground/background segmentation and masking.

Thank you! This is super helpful.

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