Many retardance pixel values are zero, or close to zero. This means that no retardance was accumulated along the ray that lead to the zero pixels. Unless the optic axis is parallel to the ray direction, the birefringence of all those voxels that the ray traversed is zero. Optimizing the birefringence and optic axis values across the entire volume can be both slow and result in an incorrect local minima.
Preferred solution
Before starting the reconstruction process, identify which voxels caused the nonzero retardance values. Then, only optimize over those voxels. Those voxels can be isolated from the volume array. Alternatively, the initial values of the remaining voxels can be set to zero.
Additional context
Experimental retardance images will need to be thresholded before extracting the nonzero pixels.
Many retardance pixel values are zero, or close to zero. This means that no retardance was accumulated along the ray that lead to the zero pixels. Unless the optic axis is parallel to the ray direction, the birefringence of all those voxels that the ray traversed is zero. Optimizing the birefringence and optic axis values across the entire volume can be both slow and result in an incorrect local minima.
Preferred solution
Before starting the reconstruction process, identify which voxels caused the nonzero retardance values. Then, only optimize over those voxels. Those voxels can be isolated from the volume array. Alternatively, the initial values of the remaining voxels can be set to zero.
Additional context
Experimental retardance images will need to be thresholded before extracting the nonzero pixels.