Calculating Volume Fraction Porosity in Thresholded Images

[JWrubel]

Hello all,

I know this is a common topic but I feel my question is different enough to warrant a new thread. I have a stack of ~200-500 tomographs (.tiff format) of what is essentially a porous, solid sphere. The images are easily thresholded/converted to binary, however the problem is that the pores are the same color (black) as the background.

I've been using the plugin "voxel counter" (Wayne Rasband, NIH) because it exactly fits my needs, i.e. it returns Thresholded voxels, total ROI voxels, and volume % thresholded voxels for the entire stack. However this plugin acts on one ROI for the entire stack where ideally, I would like to change the ROI (using the wand tool) for each slice (in order to ignore the background).

I know I could use the ROI manager, but this still involves manually selecting an ROI for hundreds of slices. Ideally I would like to tell FIJI to find the brighest pixel, do the wand tool at that point, count the thresholded voxels inside the ROI, and then move to the next slice and repeat.

Can anyone suggest a way to do this, whether it includes modifying the voxel counter plugin or perhaps a different method?

Thanks in advance,
Jake Wrubel

Example slice, I would like the ROI to include the white circle and everything inside: