Tracing the direction of individual collagen bundles from backward-scattered SHG images is much more challenging than from forward-scatter SHG images. Corneal collagen bundles changing directions cause corresponding changes in SHG images. To deconvolute and simplify indirect estimation of collagen arrangement, ImageJ software was used. Grayscale SHG images were processed by sequential application of image modifications. First, an image was processed by application of spatial frequency filters (ImageJ→ Process→ Fourier transform (FFT) → Bandpass filter;
Fig. 1). ImageJ bandpass filters have the capacity to remove both high and low spatial frequencies. The filter sets for large and small structures were set 100 and 20 pixels, respectively. Suppression stripes were set to ‘none' and tolerance of direction was set at 5%. ‘Autoscale after filtering' and ‘saturate image when autoscaling' were activated during processing. Second, the filtered images were converted to binary (ImageJ→ Process→ Binary→ Make binary). The crossing density of black and white areas in converted images were measured (ImageJ→ analyze→ gel→ plot lanes) and defined as the number of peaks crossing median cut-off intensity. This method yielded relatively constant values regardless of measurement area in the same image. The measured crossing densities at vertical midline indirectly represent the complexity of collagen bundle patterns (
Fig. 1). The higher the crossing density, the more complex the pattern is. Therefore, crossing density was designated as ‘irregularity' in this study. Irregularity was compared along differing depths (superficial, anterior, middle, and posterior central cornea) and different regions (central, peripheral, and limbal area) of cornea. Considering the normal thickness discrepancy between central, peripheral, and limbal corneas, the anterior, middle, and posterior layers were measured at 10% (superficial), 25% (anterior), 50% (middle), and 75% (posterior) depths of the central cornea, temporal peripheral cornea (approximately 4 mm away from the corneal center), and at the temporal limbus. Measurements were taken from seven corneas and each plane was measured in triplicate and mean used for analysis.