First, the z-axis is chosen perpendicular to the basilar membrane. Subsequently, base and apex of cells are indicated by landmarks. As such, the cells are approximated as a stick representation. This representation is used to calculate the 3D lengths and angles of all imaged cells. Since the OoC is not straight but spiral-shaped, the radial (y) and longitudinal (x) directions differ at each location. Therefore, circular arcs are fitted through the 3 rows of outer HCs to define the local radial (y) and longitudinal (x) direction. Novel in this approach is the 3D data of the cell position in the organ of Corti. Cell diameters and tissue areas cannot be quantified with this stick representation and need to be measured separately.
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Joris AM Soons, Anthony J. Ricci, Charles R. Steele, Sunil Puria, "Characterization of the mouse organ of Corti cytoarchitecture using a stick representation," Proc. SPIE 9303, Photonic Therapeutics and Diagnostics XI, 93031P (26 February 2015);