I’m trying to measure trabecular spaces in my bone. As previously suggested, I’m filling the background to limit the negative, background space to the interior of the bone to cut down on processing time.
(Process -> Subtract background (25 pixel rolling ball, disable smoothing). Binary -> Make binary (default binarization method and default background color).
However, after subtracting the background and binarizing the image, the thickness and spacing functions appear to be flipped, at least in the thickness/spacing maps that are generated. For example, if I tell BoneJ to calculate thickness, it’s appears as if it’s calculating spacing (thickness of the black space) and vice versa if I ask BoneJ to calculate spacing.
This reversal of thickness/spacing doesn’t happen with images that have only been thresholded and not backgrounded subtracted.
Pictures are included to help illustrate my point.
So, my questions: is there a reason this is occurring and what can I do to fix it? Alternatively, since my thickness maps are indicating that trabecular thickness is measuring the spaces in my image, can I use this value to report spacing? I just want to be sure the numbers BoneJ is giving me are actually measuring what I think it’s measuring.