The algorithm to correct the data and create the images has been described by Willemse et al.
24 All post-processing was performed in MatLab R2018a, and took approximately 3 hours per dataset. Images used in this study included intensity, local optic axis orientation, optic axis uniformity (OAxU), and cumulative phase retardation. Cumulative phase retardation images were calculated to compare to previous work on PS-OCT and are included in the
Supplementary Material. OAxU values vary between 0 and 1 and measure the anisotropy of the optic axis in a small region. Optic axes orientation images were obtained using differential Mueller calculus as originally developed by Villiger et al.
25 If there are any preceding birefringent layers of tissue with a different optic axis, the extracted optic axis for the layer underneath is affected and needs to be corrected. Instead of using Jones’ calculus
26 or constructing SO(3) rotation matrices
27 to correct for this effect, we developed a method using the same differential Mueller calculus. This method is described in the
Supplementary Material. The algorithm for automatic segmentation of the sclera and retinal pigment epithelium (RPE) can also be found in the
Supplementary Material. Automatic segmentation of the RNFL was performed using the algorithm described by Willemse et al.
24 To visualize the different imaging modalities, cross sectional intensity images were overlaid with the optic axis orientation whenever that pixel had an OAxU value > 0.5. Intensity en face images were created using the logarithmic values of the intensity and summing them along each A-line. RNFL orientation en face images were created by computing the mean of each vector element of the optic axes within the segmented RNFL. Similarly, scleral orientation en face images were created with the mean of each vector element of the optic axes over the first 30 pixels (approximately 150 µm) of the segmented sclera that had an OAxU value > 0.5. Because no automatic segmentation is available for Henle's fiber layer / the outer plexiform layer (OPL), orientation en face images were created by taking the mean of each vector element of all pixels with OAxU > 0.5 to visualize the orientation of Henle's fiber layer. Because the RNFL is very thin in the macula region, and sclera tissue is often too deep to be visualized in the macula region, this method did not obscure the signal coming from Henle's fiber layer. Cumulative optic axis images were also created to further visualize the orientation of Henle's fiber layer. In these images, the optic axis is not calculated over one pixel in depth, but over the full distance between the pixel and the surface. This was calculated by using the concurrent decomposition of the Jones matrices
J as introduced by Li et al.
27:
\begin{eqnarray*}{\rm{O}}{{\rm{A}}_{{\rm{cum}}}} &=& {\rm{imag}}\left( {\begin{array}{@{}*{1}{l}@{}} {{{\rm{J}}_{{\rm{R11}}}} - {{\rm{J}}_{{\rm{R22}}}}}\\ {{{\rm{J}}_{{\rm{R12}}}} + {{\rm{J}}_{{\rm{R21}}}}}\\ {i\left( {{{\rm{J}}_{{\rm{R12}}}} - {{\rm{J}}_{{\rm{R21}}}}} \right)} \end{array}} \right),\\
\,{\rm{with}}\,\bf{J_{\rm{R}}} &=& \frac{{{\bf{J^{\prime}}} \cdot \exp \left( { - i\,\arg \left( {{{\rm{J}}_{11}}} \right)} \right)}}{{\sqrt {\det \,\left( {{\bf{J^{\prime}}} \cdot \exp \left( { - i\,\arg \left( {{{\rm{J}}_{11}}} \right)} \right)} \right)} }}.\end{eqnarray*}
Subsequently, cumulative optic axis en face images were created by averaging the cumulative optic axis of the pixels segmented as RPE pixels to create optic axis en face images of the macular area with a higher contrast.