title: Axon tracking in serial block-face scanning electron microscopy.
abstract: Electron microscopy is an important modality for the analysis of neuronal structures in neurobiology. We address the problem of tracking axons across large distances in volumes acquired by serial block-face scanning electron microscopy (SBFSEM). Tracking, for this application, is defined as the segmentation of an axon that spans a volume using similar features between slices. This is a challenging problem due to the small cross-sectional size of axons and the low signal-to-noise ratio in our SBFSEM images. A carefully engineered algorithm using Kalman-snakes and optical flow computation is presented. Axon tracking is initialized with user clicks or automatically using the watershed segmentation algorithm, which identifies axon centers. Multiple axons are tracked from slice to slice through a volume, updating the positions and velocities in the model and providing constraints to maintain smoothness between slices. Validation results indicate that this algorithm can significantly speed up the task of manual axon tracking.
authors.affiliation: Scientific Computing and Imaging Institute, University of Utah, Salt Lake City, UT, USA. liz@sci.utah.edu
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Jurrus
authors.forename: Melissa
authors.initials: M
authors.lastname: Hardy
authors.forename: Tolga
authors.initials: T
authors.lastname: Tasdizen
authors.forename: P Thomas
authors.initials: PT
authors.lastname: Fletcher
authors.forename: Pavel
authors.initials: P
authors.lastname: Koshevoy
authors.forename: Chi-Bin
authors.initials: CB
authors.lastname: Chien
authors.forename: Winfried
authors.initials: W
authors.lastname: Denk
authors.forename: Ross
authors.initials: R
authors.lastname: Whitaker
mesh_terms: D000465:Algorithms; D000818:Animals; D001185:Artificial Intelligence; D001369:Axons / Q000648:ultrastructure*; D007089:Image Enhancement / Q000379:methods; D007090:Image Interpretation, Computer-Assisted / Q000379:methods*; D021621:Imaging, Three-Dimensional / Q000379:methods*; D008855:Microscopy, Electron, Scanning / Q000379:methods*; D010363:Pattern Recognition, Automated / Q000379:methods*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D014795:Visual Pathways / Q000196:embryology* / Q000648:ultrastructure*; D015027:Zebrafish