Filament Segmentation can be used for a globally optimal filament segmentation of 2D images with previously unknown number of filaments. Presented solution can produce sub-pixel accuracy results and handle different types of image data from different microscopy modalities.
The best way to install it is via the MOSAIC Fiji Update site, as described on the MOSAIC web page.
The algorithm is described in X. Xiao, V. F. Geyer, H. Bowne-Anderson, J. Howard, and I. F. Sbalzarini (2016).
 X. Xiao, V. F. Geyer, H. Bowne-Anderson, J. Howard, and I. F. Sbalzarini. Automatic optimal filament segmentation with sub-pixel accuracy using generalized linear models and B-spline level-sets. Med. Image Anal., 32:157–172, 2016