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):
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
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
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
Summer Institute at Lehigh University, funded by the Howard
Hughes Medical Institute. Click here for more
details on the 2009 and
2010 BDSI teams.
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.
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,
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
T. Xu, D. Vavylonis and X. Huang, "3D Actin Network
Centerline Extraction with Multiple Active Contours,"
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)
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.,
Faculty of 1000)
M. B. Smith, H. Li, T.
Shen, X. Huang, E. Yusuf, and D. Vavylonis, "Segmentation and Tracking of Cytoskeletal Filaments using Open Active
67 693-705 (2010).
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.
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.