Teeth slice geometry troubles in BoneJ

Hello, I am using slice geometry in BoneJ to analyze dog teeth. I am working with stacks of microCT images of the teeth. It appears the output of measurements is inaccurate. I believe it is picking up pixels outside of the actually sample. The major and minor axes annotated on the stack file and 3D rendering suggests they are outside of the area of interest. Here is my workflow:

  1. upload stack
  2. duplicate stack
  3. crop stack
  4. convert to 8 bit
  5. adjust ww/wl
  6. run slice geometry.

I have several images that show the issue but can’t seem to upload them. Any help anyone could provide is greatly appreciated. If someone could direct me on the process to upload images, I’m happy to do so.

Thank you,


This would really help. Even better would be screenshots of each step 1-6 above, and a macro that you record while doing it (Plugins>Macro>Record…).

If your input images are 16-bit there is no need for step 4. Better is either to run directly on the 16-bit data with pixel min and max values that you specify, or to apply a threshold and run on binary images.

What is this?

Thank you for the help, Michael.

The images are uploaded into ImageJ as a 32 bit file. In order to adjust ww/wl (window width and level) in order to remove a beam hardening artifact, I convert them to 8 bit file.

I then run the slice geometry feature in BoneJ and here is the result.

Thank you so much for the help!

Jason S.

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Looks like it should be running OK. You can check the Bone Min and Bone Max values visually by running Adjust > Threshold, inputting the default values 126 and 255, to see which parts of the specimen are included. It’s likely that some parts of the dentine and cementum are excluded.

You should also do a sensitivity analysis to check how your window level and width values (converting 32-bit to 8-bit), and subsequent Bone Min and Max values, affect the readout values.