Tracking Tubular Shaped ObjectsCISMM: Computer Integrated Systems for Microscopy and Manipulation

Collaborators: Bob Goldstein, Erin McCarthy, Michael Stadermann, Sreeja Asokan

Project Lead: Russell M. Taylor II Investigators: Yonatan Fridman, Stephen Pizer

http://www.cs.unc.edu/Research/nano/cismm/download/tubetracer/

October 2002

2D Applications of Cores

3D Applications of Cores

Nanotube Conductivity

Figure 1: AFM image of a multi-wall carbon nanotube.

Figure 2: Corresponding image showing conduc-tivity at all locations.

Figure 3: Original AFM image (in grayscale) with computed core and two user-defined dots.

Figure 4: Conductivity values plotted along the length of the computed core/backbone. Maximum, average, and minimum values are taken over the nanotube’s cross-sections.

Solution:: Compute the core of the nanotube and plot conductivity Compute the core of the nanotube and plot conductivity data from corresponding locations in the conductivity image. Allowdata from corresponding locations in the conductivity image. Allow

Actin Under DEP Force

Figure 5: Actin filaments (white) between parallel electrodes (black) when a DEP force is on (left) and off (right).

Solution:Solution: Compute the cores of the filaments and plot Compute the cores of the filaments and plot histograms of the core tangent directions at all core histograms of the core tangent directions at all core sample points.sample points.

Figure 6: Orientations of actin filaments wher a DEP force is on (left) and off (right). The left histogram shows alignment at an orientation of about two radians, which is perpendicular to the electrodes.

Microtubule Behavior During Asymmetric Cell Division

Problem:Problem:• During asymmetric cell division the mitotic spindle positions itself asymmetrically, and microtubules have an During asymmetric cell division the mitotic spindle positions itself asymmetrically, and microtubules have an effect on this positioning.effect on this positioning.• The problem is to determine the role of the microtubules on asymmetric spindle positioning by analyzing the The problem is to determine the role of the microtubules on asymmetric spindle positioning by analyzing the stability of the microtubules at the cell cortex.stability of the microtubules at the cell cortex.

Solution:Solution:• Movies are taken of microtubules in a cortical plane (Fig. 7). Microtubules appear as small dots ofMovies are taken of microtubules in a cortical plane (Fig. 7). Microtubules appear as small dots of

Problem:Problem: Understand Understand how conductivity how conductivity changes with location changes with location along a nanotube and along a nanotube and with orientation of the with orientation of the nanotube.nanotube.

the user to click on points of interest the user to click on points of interest in the plot, then mark corresponding in the plot, then mark corresponding locations on the core.locations on the core.

Problem:Problem: Quantify how Quantify how responsive actin filaments responsive actin filaments are to a dielectrophoresis are to a dielectrophoresis (DEP) force by determining (DEP) force by determining how well they align when how well they align when placed in a force field.placed in a force field.

Figure 7: Imaging of microtubules in a cortical plane during cell division.

Figure 8: Converting a set of movie frames into a single 3D image.

fluorescence in these movies, and the residence time of fluorescence in these movies, and the residence time of a microtubule at the cortex can be determined by a microtubule at the cortex can be determined by computing the number of movie frames during which it’s computing the number of movie frames during which it’s visible in the plane of focus.visible in the plane of focus.

• Given a set of movie frames with dots that persist Given a set of movie frames with dots that persist through multiple frames, microtubule stabilities are through multiple frames, microtubule stabilities are computed automatically using 3D cores:computed automatically using 3D cores:• By stacking the frames we can create a 3D image in By stacking the frames we can create a 3D image in which each persisting dot appears as a tube (Fig. 8).which each persisting dot appears as a tube (Fig. 8).• We track the tubes in the 3D image using cores and We track the tubes in the 3D image using cores and see how long (spatially) each tube is – this tells us see how long (spatially) each tube is – this tells us how long (temporally) each dot persists (Fig. 9).how long (temporally) each dot persists (Fig. 9).

Figure 9: The image from Fig. 7 with microtubule dots in the anterior region automatically located and circled. Colors indicate individual microtubule stability.

1. Aylward, SR, E Bullitt (2002). Initialization, noise, singularities, and scale in height ridge traversal for tubular object centerline extraction. IEEE Transactions on Medical Imaging, 21: 61-75.

2. Aylward, SR, SM Pizer, E Bullitt, D Eberly (1996). Intensity ridge and widths for tubular object segmentation and description. IEEE Workshop on Mathematical Methods in Biomedical Image Analysis, 56: 131-138.

3. Pizer, SM, D Eberly, BS Morse, DS Fritsch (1998). Zoom-invariant vision of figural shape: The mathematics of cores. Computer Vision and Image Understanding, 69: 55-71.

This work is built upon other work done in MIDAG, including that of Aylward, Bullitt, Eberly, Fritsch, Furst, Morse, and Pizer. Specifically, Aylward and Bullitt [1], [2] use a multi-scale image intensity ridge traversal method in which they separately search for position and width information, and define orientation implicitly. Also see [3] for more information on the mathematics of cores.