Localizing and extracting filament distributions from microscopy images

J Microsc. 2015 Apr;258(1):13-23. doi: 10.1111/jmi.12209. Epub 2014 Dec 30.


Detailed quantitative measurements of biological filament networks represent a crucial step in understanding architecture and structure of cells and tissues, which in turn explain important biological events such as wound healing and cancer metastases. Microscopic images of biological specimens marked for different structural proteins constitute an important source for observing and measuring meaningful parameters of biological networks. Unfortunately, current efforts at quantitative estimation of architecture and orientation of biological filament networks from microscopy images are predominantly limited to visual estimation and indirect experimental inference. Here, we describe a new method for localizing and extracting filament distributions from 2D microscopy images of different modalities. The method combines a filter-based detection of pixels likely to contain a filament with a constrained reverse diffusion-based approach for localizing the filaments centrelines. We show with qualitative and quantitative experiments, using both simulated and real data, that the new method can provide more accurate centreline estimates of filament in comparison to other approaches currently available. In addition, we show the algorithm is more robust with respect to variations in the initial filter-based filament detection step often used. We demonstrate the application of the method in extracting quantitative parameters from confocal microscopy images of actin filaments and atomic force microscopy images of DNA fragments.

Keywords: Biological filament networks; centreline curvature; curvilinear structures; local network topology.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Actin Cytoskeleton / ultrastructure
  • Algorithms
  • Cytoskeleton / ultrastructure*
  • Diffusion
  • Microscopy / methods*
  • Microscopy, Atomic Force / methods*
  • Microscopy, Confocal / methods*