DSeg: A Dynamic Image Segmentation Program to Extract Backbone Patterns for Filamentous Bacteria and Hyphae Structures

Microsc Microanal. 2019 Jun;25(3):711-719. doi: 10.1017/S1431927619000308. Epub 2019 Mar 21.


Analysis of numerous filamentous structures in an image is often limited by the ability of algorithms to accurately segment complex structures or structures within a dense population. It is even more problematic if these structures continuously grow when recording a time-series of images. To overcome these issues we present DSeg; an image analysis program designed to process time-series image data, as well as single images, to segment filamentous structures. The program includes a robust binary level-set algorithm modified to use size constraints, edge intensity, and past information. We verify our algorithms using synthetic data, differential interference contrast images of filamentous prokaryotes, and transmission electron microscopy images of bacterial adhesion fimbriae. DSeg includes automatic segmentation, tools for analysis, and drift correction, and outputs statistical data such as persistence length, growth rate, and growth direction. The program is available at Sourceforge.

Keywords: MATLAB; filamentous; hyphae; image segmentation; software.

MeSH terms

  • Algorithms
  • Bacteria / cytology*
  • Bacteria / growth & development*
  • Bacterial Adhesion
  • Computational Biology / methods*
  • Fimbriae, Bacterial
  • Image Processing, Computer-Assisted / methods*
  • Microscopy / methods*
  • Microscopy, Electron, Transmission
  • Microscopy, Video / methods
  • Software
  • Workflow