Making areas 'data' free

[Charlene Greenwood]

Hi,

I am currently using ImageJ and the plugin BoneJ to measure parameters associated with trabecular bone. My specimens have previously undergone mechanical testing so have holes and notches within them. I have subtracted these void areas using CT software, which accepts that there is no data within these areas and does not include the 'black voids' I have created during analysis. Unfortunately ImageJ/ Bone J does not do this and includes these voids during the analysis. Is there any way I can tell ImageJ that these voids are essentially 'data free' and not to be included in the analysis, without cropping the image??

Hope this all makes sense and any help would be appreciated. I have included an image to try to illustrate what I mean.


Thank you.