Analysis of individual full cells. Analysis of individual full cells. A, Territorial volume of each cell is determined by placing a polygon around all of the extreme points of the cell. B, The user decides which skeletonization method to use and which images to save (including: original cell, skeleton, branch points, and end points). Each full cell (C) is then processed individually to generate a 3D skeleton, keeping either all branches (D), or only major branches (E). In skeleton figures, colors indicate order of connectivity (red = primary, yellow = secondary, green = tertiary, and blue = connected to endpoint). F, After processing all cells, the program outputs territorial volume, cell volume, ramification index (calculated as territorial volume/cell volume), number of endpoints and branch points, as well as average, maximum, and minimum branch length for each cell. A complete list of branch lengths for each cell can also be generated. Elisa M. York et al. eNeuro 2018;5:ENEURO.0266-18.2018 ©2018 by Society for Neuroscience