Provided are embodiments of a method for performing automatic analysis of cross-sections of micro-channels. Embodiments includes receiving tomography scan data, aligning the tomography scan data, and extracting channels from a slice of the tomography scan data to create an isolated slice of the extracted channel. Embodiments also include determining surface voxels for the extracted channels, and determining an area defined within the surface voxels for each of the extracted channels. Embodiments include determining a contribution of the surface voxels for each of the extracted channels to the cross-section of the extracted channels, and outputting cross-section information based on the contribution of the surface voxels. Also provided are embodiments of a system for performing automatic analysis of cross-sections of micro-channels.