Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported Yes Drexel University NITRC Axonal Beading and Microtubule Quantification Yes MATLAB Interactive image analysis software for quantifying axonal beading morphology and focal microtubule loss using phase and fluorescent images of a neuron. Purpose: Focal axonal beading and focal disruption of microtubule structure are characteristic to traumatic axonal injury. We reproduced these morphological and structural changes in our in vitro model system [Kilinc, Gallo, Barbee, 2008. Exp. Neurol. 212:422–430]. In order to measure bead formation objectively, an observer-independent quantification of beading was necessary. In addition, a quantitative measure for the extent of co-localization of axonal beads and microtubule disruptions was required to establish a causal relationship between focal cytoskeletal damage and bead formation. In this paper we describe Matlab-based, interactive image analysis programs for axonal beading quantification and co-localization analysis. Injury-induced increases in the axonal beading could be successfully detected using the bead analysis program. Axonal Beading and Microtubule Quantification Optical Imaging, Microscopy, Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported, Quantitative Shape Analysis, MATLAB http://www.nitrc.org/projects/axonal_beading/