On Apr 25, 2014, at 5:01 PM, Charlene Greenwood wrote:
> 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??
ImageJ ignores NaN pixels so you need to set the voids to NaN. There are at least two ways to do this:
1. Use Image>Type>32-bit to convert the image to float. Use Image>Adjust>Threshold to select everything except the voids, click "Apply" and check "Set background pixels to NaN" in the dialog.
2. Use Image>Type>32-bit to convert the image to float. Use Image>Adjust>Threshold to select the voids, create a selection using Image>Selection>Create Selection, then use Process>Math>Set to set the pixels to NaN.
-wayne
> 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.
>
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