(a) The plastic foam used to fabricate the phantom. The plastic foam was embedded in silicone rubber. (b) and (c) are 3-D reconstructions of OCT intensity without (b) and with (c) computational refocusing. The red arrow indicates the depth location of Fig. 2. The 3-D scale bar in (b) denotes 500 μm.

Intensity en face images without (a), and with (b) computational refocusing. (c) and (d) are the corresponding birefringence images, and (e) and (f) are magnified images of the yellow-box regions in (c) and (d), respectively. Scale bar denotes 500 μm. (g) Intensity line profiles at the red line in (a) and (b), where blue and orange curves denote the profiles without and with refocusing, respectively. Evident improvements in resolution following computational refocusing can be observed in the images and the plot.

Zebrafish imaging results. (a)-(c) are the intensity, birefringence, and DOPU images without refocusing, respectively. (d)-(f) are the corresponding images with computational refocusing. Orange arrowheads indicate particles with strong reflection. Red arrows indicate the gill filament and yellow arrows the operculum. Black arrows indicate projection artifacts of birefringence and DOPU caused by structure superior to the imaged slice. White arrows indicate areas adjacent to the operculum, which might be operculum musculature or adductor mandibulae. Abbreviations: O, operculum; S, skin; GF, gill filament; PM, pectoral fin muscle. Scale bar denotes 500 μm.

Original (first row) and computationally refocused (second row) OCT volumes of the porcine muscle sample. (a) and (b) 3-D reconstructed cut-away volumes. (c)-(h) are en face slices extracted from depths of 0-, 0.38-, and 1.06- mm from the surface. Scale bars in (a) and (c) denote 500 μm.

Original (first column) and computationally refocused (second column) en face porcine triceps brachii muscle images. The images are extracted from a depth away from the depth of focus. The first to third columns are the intensity, birefringence, and DOPU images, respectively. (g)-(l) are corresponding magnified images of the regions outlined by black-dashed boxes, where the left images are without refocusing and the right ones are with computational refocusing. Red arrows in (a) and (b) denote a hollow region, which exhibits evident sharpening following computational refocusing. Black arrowheads in (i) and (k) denote birefringence and DOPU artifacts. Scale bar denotes 500 μm.

Comparisons of physically/computationally in-focus and physically/computationally defocused images. (a) and (e) are physically defocused images, and (b) and (f) are corresponding computationally refocused images. (d) and (h) are physically in-focus images, while (c) and (g) are computationally defocused versions of these images. The white-box insets are the magnified images of the black-box regions. The black arrows indicate the polarization artifacts. Yellow boxes denote four manually selected areas with a 15 × 15-pixel size where artifacts are observed. Scale bar denotes 500 μm.

Mean birefringence (a) and DOPU (b) at four regions in Fig. 6 (yellow boxes). The mean values were computed as the mean of the mean values of each region. Bars indicate the standard deviations among the four means of the four regions.

The dependency of the mean birefringence (a) and DOPU (b) on the amount of defocusing. Vertical axes indicate the mean birefringence (a) and DOPU (b) over the whole en face field except for low-intensity pixels. Each plot corresponds to different samples, with the orange rectangles, gray circles, and yellow squares denoting the first and second porcine muscle samples and zebrafish, respectively. As the absolute defocus increases, the mean birefringence increases and the mean DOPU decreases.

Artifacts that appear at the periphery of the en face field. The raw data are identical to what appear in Fig. 6. The first-to-third columns show the computationally refocused en face intensity, birefringence, and DOPU images, respectively. For (a)-(c), zero-fields were padded to the periphery of the image before the first Fourier transform of the computational refocusing process. On the other hand, zero-padding was not applied for (d)-(f). The white insets are magnifications of the black-box regions. Arrows in (d)-(f) indicate artifacts at the periphery. This artifact can be removed by zero-padding. The scale bar denotes 500 μm.

Defocus estimates are plotted against the sample depth. (a) Four plots represent four polarization channels, where each column and row correspond to each input and output polarizations, respectively. The defocus estimates were performed independently to each polarization channel. Orange crosses and blue triangles indicate the results with and without bulk-phase error correction, respectively. The red line is a linear regression line obtained from the data at the green region. The blue region indicates the region within the depth-of-focus (DOF). The data with bulk-phase error correction well agree with the regression line outside of DOF, while systemic departure can be found within the DOF as expected. (b) shows a representative cross-sectional OCT of the scattering phantom without refocusing.