I have been working through various combinations of parameter values and pre-processing for Ellipsoid Factor, in an attempt to achieve a fill percentage above 90%. This is on the advice I have read in this forum. Fill percentage >90% is stated to be an adequate representation of the bone in the sample.
I have altered the following values through the ranges at appropriate increments for each:
Skeleton points / ellipsoid from 1 to 5
Vectors from 100 to 300
Threshold lower value 50, 65, 70, 75, 80 and 89 (89 is the auto value). Upper threshold value always 255
Maximum drift 3 to 4
Iterations 100 to 300
Sampling increment 0.25 to 0.435 (the default value is 0.435)
The dataset I am working with is a 140 slice rat tibia trabecular VOI created in CTan. I use file>import>image sequence, and set it to 8-bit greyscale. I then threshold the dataset and select black background, b&w, prior to running the ellipsoid factor from the bonej menu.
My optimum parameters have been:
skeleton points / ellipse 1
sampling increment 0.21
fill percentage = 83.2%
Skeleton points / ellipse 1
sampling increment 0.3
fill percentage = 90.26%
- Surely lowering the threshold is not the way to go about this? Doesn’t that mean that I am including way too much soft tissue in the binarization, and so the sample isn’t representing the bone adequately?
- If I decide the reasoning in 1) is good and I need to keep the threshold around 89, how can I improve the fill percentage past ~83%? Is it by running pre-processing like despeckle, or an erosion then a dilation? I don’t know how much pre-processing is an acceptable amount to keep the sample adequately representing the bone.
Thanks for taking the time to read all this.