ImageJ

JFilament is an ImageJ plugin for segmentation and tracking of 2D and 3D filaments in fluorescenece microscopy images. The main algorithm used in Jfilament is "Stretching Open Active Contours".

For user instructions go to http://athena.physics.lehigh.edu/jfilament.

This work was supported by NIH and by the Biosystems Dynamics Summer Institute at Lehigh University.

The code was developed by Matt Smith, melkor@orangepalantir.org

References:

M. B. Smith, H. Li, T. Shen, X. Huang, E. Yusuf, and D. Vavylonis, "Segmentation and Tracking of Cytoskeletal Filaments using Open Active Contours," Cytoskeleton 67:693-705 (2010) [1]

H. Li, T. Shen, M. B. Smith, I. Fujiwara, D. Vavylonis, and X. Huang, "Automated Actin Filament Segmentation, Tracking, and Tip Elongation Measurements based on Open Active Contour Models," In Proc. of the IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI-09, Boston, 2009 [2]