 SNT (neuroanatomy software)

SNT is an ImageJ framework for tracing, displaying and quantitatively analyzing branching structures in multidimensional images. It provides editing and automated tracing tools as well as a scripting interface. Its computational components also support filamentous structures outside the package's original application domain.^[ref]

A trace encodes connected sample points rather than merely an image of a bright line. For an original geometric example, take successive physical coordinates $(0,0,0)$, $(3,0,0)$ and $(3,4,0)$ in micrometres. The trace's length is the sum of its two line segment lengths,whereas the endpoint Euclidean distance is $d=\sqrt{3^2+4^2}=5\mu \mathrm{m}$. The ratio $d/L=5/7\simeq 0.714$ distinguishes a bent trace from a straight one with the same endpoints. SNT's metrics documentation defines path/branch length through internode distances and branch contraction through this endpoint-distance-to-path-length ratio.^[ref]

Those calculations require calibrated coordinates and the intended connectivity. Rescaling image axes changes lengths; connecting the wrong endpoints changes the traced object. The framework's Sholl analysis is a different summary: it produces a Sholl profile of radial intersections. The fact that a Sholl profile does not determine rooted tree topology explains why a profile cannot replace the connected trace when the question concerns its branching structure. This example concerns software data and geometry, not measured anatomy.