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Automatic optimal filament segmentation

Filament Segmentation (ImageJ)
Author MOSAIC Group, Center for Systems Biology Dresden (CSBD), Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany.
Update site MOSAIC ToolSuite
Maintainer Krzysztof.Gonciarz
Source MPI-CBG git
Initial release 2016
Development status active
Category Segmentation
Website MosaicSuite

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[1]).


  1. 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