Microscopic Image Analysis


We developed Speckle TrackerJ, an ImageJ tool for analyzing trajectories of point-like particles in fluorescence microscopy time-lapse movies.  Manual and computer-assisted techniques allow robust tracking of speckles in different situations.  Examples of uses of the program include measurements of the diffusion coefficient of capping proteins in the lamellipodium, appearance and disappearance events of fluorescently-labeled vesicles to supported lipid bilayers, and tracking of  single lipids from the fused vesicle on the bilayer (models and software: M.B. Smith; experimental work by E. Karatekin, A. Gohlke, H. Mizuno, N. Watanabe).


We also develop methods to segment and track filamentous structures in microscopic images, in collaboration with the group of Xiaolei Huang (CSE, Lehigh University):


We developed SOAX, an open source software tool to extract the centerlines and junctions of filamentous networks in 2D/3D images. The underlying method of SOAX uses multiple Stretching Open Active Contours (SOACs) that are automatically initialized at image intensity ridges and then stretch along the centerlines of filaments in the network. SOACs can merge, stop at junctions, and reconfigure with others to allow smooth crossing at junctions of filaments. SOAX provides 3D visualization for exploring image data and visually checking results against the image. SOAX provides quantitative analysis functions and interactive manual editing to improve the extraction results.


We also developed JFilament, an open source interactive ImageJ plugin for segmentation, tracking, and visualization of individual fibers. The program uses open active contours to quantify cytoskeletal structures imaged by fluorescence microscopy in two and three dimensions. Examples of applications of JFilament include studies of actin elongation rates using Total Internal Reflection Fluorescent Microscopy.


A set of ImageJ plugins (LEAP) can be used to quantify cell shape and intensity near the cell edge.


This work was supported by NIH, grants R01GM098430, R21GM083928, the HFSP, and the Biosystems Dynamics Summer Institute at Lehigh University, funded by the Howard Hughes Medical Institute. Click here for more details on the 2009 and 2010 BDSI teams.




  1. T. Xu, D. Vavylonis, F.-C. Tsai, G. H. Koenderink, W. Nie, E. Yusuf, I-J. Lee, J.-Q. Wu, X. Huang, "SOAX: A software for quantification of 3D biopolymer networks," (SCIENTIFIC REPORTS, 2015).
  2. T. Xu, D. Vavylonis and X. Huang, "3D Actin Network Centerline Extraction with Multiple Active Contours," MEDICAL IMAGE ANALYSIS 18:272-284 (2014).
  3. G. L. Ryan, N. Watanabe and D. Vavylonis, "Image Analysis Tools to Quantify Cell Shape and Protein Dynamics near the Leading Edge" (Cell Structure and Function, 2013)  
  4. M. B. Smith, E. Karatekin, A. Gohlke, H. Mizuno, N. Watanabe and D. Vavylonis, "Interactive, computer-assisted tracking of speckle trajectories in fluorescence microscopy: application to actin polymerization and membrane fusion," BIOPHYS J., 101:1794-1804 (2011). (Evaluated in Faculty of 1000)  
  5. 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).
  6. T. Xu, H. Li, T. Shen, N. Ojkic, D. Vavylonis, X. Huang "Extraction and analysis of actin networks based on open active contour models," in Proc. of the IEEE Int'l Symposium on Biomedical Imaging: From Nano to Macro, ISBI'11, Chicago, 2011.
  7. H. Li, T. Shen, D. Vavylonis, X. Huang, "Actin Filament Segmentation Using Spatiotemporal Active-Surface and Active-Contour Models," International Conf. on Medical Image Computing and Computer Assisted Intervention, MICCAI'10, Beijing, 2010.
  8. H. Li, T. Shen, D. Vavylonis, X. Huang, "Actin Filament Tracking Based on Particle Filters and Stretching Open Active Contour Models," International Conf. on Medical Image Computing and Computer Assisted Intervention, MICCAI'09, London, 2009.
  9. 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 Int'l Symposium on Biomedical Imaging: From Nano to Macro, ISBI'09, Boston, 2009.



Last update: 3/4/15