Motivation: Quantitative image analysis of growing filamentous fungi and prokaryotes are important to detect and evaluate morphological effects of growth conditions, compounds and mutations. However, analysis of time-series image data is often limited by the ability of the algorithms to accurately segment structures that are complicated or if an organism is within a crowded population. To overcome these issues we present DSeg; an image analysis program designed to process time-series image data as well as single images to find multiple filamentous structures e.g., filamentous prokaryotes, yeasts and molds using a dynamic segmentation approach. DSeg automatically segments and analyzes objects, includes drift correction, and outputs statistical data such as persistence length, growth rate and growth direction. Availability and implementation: DSeg is a free open-source program written in MATLAB. DSeg can be downloaded as a package from https://sourceforge.net/projects/dseg-software. Contact: magnus.andersson@umu.se and hanqing.zhang@umu.se Supplementary information: Supplementary data are available at online.