FIJI (https://imagej.net/Fiji) is an image processing package—a "batteries-included" distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis.
FIJI can be used to post-process raw X-ray CT images of particles to obtain "cleaned" binary (black/white) stack images. Then the voxel coordinates of the stack images can be exported for constructing the bonded-sphere DEM particle geometry templates as input for LIGGGHTS-INL.
A concise user tutorial is provided.
File -> Import -> Image Sequence
Select region. Then do
Image -> Crop
We recommend saving the cropped image sequence in TIFF and load it again for the following operations. This saves computer memory if the memory limit is a concern.
Only good with high-contrast images. Low-contrast images like those of biomass should not use any automatic thresholding.
Image -> Adjust -> Threshold
Low-contrast images like those of biomass should require manual thresholding.
Process -> Binary -> Make Binary
Equivalent to auto threshholding. Should not apply to low-contrast images like those of biomass.
Process -> Noise -> Despeckle
Process -> Subtract Background
Do not subtract background if already binarized.
Plug-ins -> 3D Viewer
File -> Save As -> Image Sequence
Analyze -> Tools -> Save XY Coordinates (save all slices)