Branch indices of points on curves (introduced by Urysohn and Menger) are of basic importance in the mathematical theory of curves, defined in Euclidean space. This paper applies the concept of branch points in the 3D orthogonal grid, motivated by the need to analyze curve-like structures in digital images. These curve-like structures have been derived as 3D skeletons (by means of thinning). This paper discusses approaches of defining branch indices for voxels on 3D skeletons, where the notion of a junction will play a crucial role. We illustrate the potentials of using junctions in 3D image analysis based on a recent project of analyzing the distribution of astrocytes in human brain tissue.