Automated Axon Tracking of 3D Confocal Laser Scanning ...

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2.1 Tracking the Axons in the MIP ImageA simple dataset is shown in Figure 1, containing two axons shown by red and blue structures.Since such a dataset is formed by stacking a sequence of cross-sectional images, each point onthe centerlines of the axons corresponds to one cross-sectional slice in the stack of data. As seenin Figure 1, there are several points where the axons seem to cross each other. But when seenfrom a cross-sectional point of view, it is clear that they do not in fact intersect.Figure 1: An example of a stack of cross-sectional images of two axons.The MIP is just a way of visualizing the axons present in the stack of data. As mentionedearlier, the MIP image is the projection of the maximum intensities along a particular directiononto a plane perpendicular to it. Figure 1 shows the three orthogonal directions along which theMIP images could be found. The algorithm begins after the user selects one of the three possibleMIP images of the dataset having the clearest details. Figure 2 shows the three MIP images in thethree orthogonal directions in one such dataset. Since the MIP image along Z-axis provides theclearest view of the individual axons, and hence is the best for analysis, it has been used in8
tracking the centerlines. After an MIP image is chosen, it is preprocessed to enhance the edges ofthe structures.(a)(b)(c)Figure 2 - The Maximum Intensity Projection Images: (a) MIP along Y-axis, (b) MIP along Z-axis, and (c) MIPalong X-axis. The scale bar in (a) corresponds to 3μm. The scale bars in (b) and (c) correspond to 6μm.The method described in (Can et al., 1999) is adopted to track the centerlines of the axons inthe edge-enhanced MIP image. In order to automate the initialization of the tracks, a set of seedpoints is defined on the MIP image. They serve as starting points and guide the tracking9
Page 2 and 3: AbstractThis paper presents a new a
Page 4 and 5: the 3D stack. Several automatic alg
Page 6 and 7: Track the centerlines in the MIP im
Page 10 and 11: algorithm, and therefore must be in
Page 12 and 13: towards the center. Similarly, all
Page 14 and 15: algorithm. The blue line in Figure
Page 16 and 17: To avoid this problem, we introduce
Page 18 and 19: (a)(b)(c)Figure 7 - Segmentation of
Page 20 and 21: distribution and used to train the
Page 22 and 23: After the region of interest is ide
Page 24 and 25: The number of cross-sections to be
Page 26 and 27: (e)Figure 10 - Tracking results in
Page 28 and 29: Figure 11 - Tracking results in dat
Page 30 and 31: In comparison with the manual track
Page 32 and 33: algorithm worked for five consecuti
Page 34 and 35: dataset in a direction normal to th
Page 36 and 37: ReferencesAbramoff M.D., Magelhaes,
Page 38: Imaging. 24(12), 1529- 1539.Wang M.

Automated Axon Tracking of 3D Confocal Laser Scanning ...

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