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

Once the hybrid algorithm tracks all the axons in the dataset, two kinds of segments ofcenterlines result: fragments that were tracked using the template-based approach and those thatwere tracked using a sequence of cross-s ectional slices. In order to build the 3D model of thecenterlines, we need to locate the third dimension of each of these centers. Since the centerlinestracked using the template-based approach have no cross-over ambiguity, the third dimensioncan be easily found by searching for the local maximum intensity pixel in the correspondingslices in the dataset. In the latter case, the two dimensions of the centers of the segmentedregions, along with the slice number, give us the three dimensions of the centers. The results ofthe 3D reconstruction of centerlines of axons in three datasets are shown in the next section. Theresults are validated with the manual tracking results and are compared with the repulsive snakealgorithm for robustness.3. ResultsThree datasets were analyzed using the hybrid algorithm proposed in this paper. The centerlinesof the axons are presented in both two dimensions in the MIP image and in the three-dimensionaldomain. The various parameters that were manually initialized for the datasets are:• The number of cross-sectional slices in the dataset.• The MIP image of the dataset to be analyzed and the approximate maximum width of theaxons in the MIP image.• The resolution of the grid for the automatic detection of seeds in the MIP image for the 2Ddirectional template based tracking and the step size of the algorithm.• The initial seed points for the segmentation algorithm in the first axon cross-section eachtime when an axon cross-over is detected.23